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A5-miseq is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies.
an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation.
Mass screening of contigs for antibiotic resistance genes
an abundance-based tool for binning metagenomic sequences.
(Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
(Another Gff Analysis Toolkit) a suite of tools to handle gene annotations in any GTF/GFF format.
(Ancestry and Kinship Toolkit) a statistical genetics tool for analysing large cohorts of whole-genome sequenced samples. It provides a handful of useful statistical genetics routines using the htslib API for input/output. This means it can seamlessly read BCF/VCF files and play nicely with bcftools.
an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.
AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
(Advanced Normalization Tools) extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized multimodality image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to …
an open-source, community-driven analysis and visualization platform for ‘omics data. Its interactive interface facilitates the management of metagenomic contigs and associated data for automatic or human-guided identification of genome bins and their curation.
ARAGORN identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf.
ARIBA: Antibiotic Resistance Identification By Assembly
a command-line genome browser running from terminal window and solely based on ASCII characters.
Get assembly statistics from FASTA and FASTQ files.
trim adapters from high-throughput sequencing reads.
AUGUSTUS is a gene prediction program for eukaryotes that can be used as an ab initio program, which means it bases its prediction purely on the sequence.
(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
rapid and standardized annotation of bacterial genomes & plasmids.
bam2fastx provides conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.
bam-readcount generates metrics at single nucleotide positions.
BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
Barrnap predicts the location of ribosomal RNA genes in genomes. (bacteria, archaea, metazoan mitochondria and eukaryotes.)
is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files. Bazam is a smarter way to realign reads from one genome to another. If you've tried to use Picard SAMtoFASTQ or samtools bam2fq before and ended up unsatisfied with complicated, long running inefficient pipelines, bazam might be what you wanted. Bazam will output FASTQ in a form that can …
a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving.
provides best-practice pipelines for automated analysis of high throughput sequencing data with the goal of being quantifiable, analyzable, scalable and reproducible. The development process is fully open and sustained by contributors from multiple institutions. Bioinformaticians, biologists and the general public should be able to run these tools on inputs ranging from research materials to clinical samples to personal genomes.
Prioritize small variants, structural variants and coverage based on biological inputs. The goal is to use pre-existing knowledge of relevant genes, domains and pathways involved with a disease to extract the most interesting signal from a set of high quality small or structural variant calls. Given information on coverage, it will be able to identify poorly covered regions in potential genes of interest.
bcbio-variation is a toolkit to analyze genome variation data, built on top of the Genome Analysis Toolkit (GATK) with Clojure. It supports scoring for the Archon Genomics X PRIZE competition and is also a general framework for variant file comparison. It enables validation of variants and exploration of algorithm differences between calling methods by automating the process involved with comparing two sets of variants. …
Parallel merging, squaring off and ensemble calling for genomic variants. Provide a general framework meant to combine multiple variant calls, either from single individuals, batched family calls, or multiple approaches on the same sample. Splits inputs based on shared genomic regions without variants, allowing independent processing of smaller regions with variant calls.
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each …
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses …
(Binding and Expression Target Analysis) a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
is a compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples. It can be considered as an alternative to genotype-only BCFv2. BGT is more compact in size, more efficient to process, and more flexible on query.
A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well.
an extension to Brian Kernighan's awk, with added support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q, and TAB-delimited formats with column names along with new built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk should behave exactly like the original BWK awk.
tools for early stage NGS alignment file processing including fast sorting and duplicate marking.
tools to analyze and comprehend high-throughput genomic data.
Installation Client for the BioGrids software collection.
subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.
The bioinfokit toolkit aims to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments.
a set of tools for biological computation written in Python by an international team of developers.
a set of tools for the time-efficient analysis of Bisulfite-Seq (BS-Seq) data. Bismark performs alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls at the same time.
BLASR (Basic Local Alignment with Successive Refinement) maps Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. It uses the disk streaming k-mer counting algorithm contained in the GATB library, and inserts solid k-mers in a bloom-filter. The correction procedure is similar to the Musket multistage approach. Bloocoo yields similar results while requiring far less memory: as an example, it can correct whole …
aka Best Match Tagger is for removing human reads from metagenomics datasets
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets.
the Amazon Web Services (AWS) SDK for Python, which allows Python developers to write software that makes use of Amazon services like S3 and EC2. Boto provides an easy to use, object-oriented API as well as low-level direct service access.
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs.
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatbility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
Bam and Variant Analysis Tools
(Burrows-Wheeler Aligner) a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
is a command-line tool for converting 3D images between common file formats.
Cactus is a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. The correction phase will improve the accuracy of bases in reads.
a tool for calling copy number variants (CNVs) from human DNA sequencing data.
is a Python package designed to make drawing maps for data analysis and visualisation easy.
Clusters and compares protein or nucleotide sequences
a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
is a publicly available repository of curated receptors, ligands and their interactions.
Keywords:
Other
is a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

Permission to use with BioGrids given by 10X Genomics: ##- Please type your reply above this line -## Your request (71045) has been updated. To add additional comments, reply to this email. David Lin (10x Genomics) Oct 30, 2020, 7:03 PDT HI Jim Thanks for providing more details. Biogrids looks like a very useful service. It looks like you are just making it easier for users to install the command line cellranger package. Users would continue to use the native cellranger command line interface. Yes, this use case would be permissable as long as you clearly state that the installation package is not provided or supported by 10x Genomics. Please note, the 10x EULA still applies. You could probably just add this to the description in your docs. You could link out to the to the EULA here: https://support.10xgenomics.com/docs/license I hope this helps clarify. Best, Dave Dave Lin 10X Genomics Head, Software Field Operations James Vincent Oct 29, 2020, 14:45 PDT

The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.
a set of analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Single Cell ATAC data.
is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial …
Ultrafast and accurate clustering through imputation and dimensionality reduction for single-cell RNA-seq data.
Circular RNA analysis toolkits
Circlator is a tool to circularize genome assemblies. The input is a genome assembly in FASTA format and corrected PacBio or nanopore reads in FASTA or FASTQ format. Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.
Circos is a software package for visualizing data and information. It visualizes data in a circular layout
fast, accurate and versatile k-mer based classification system.
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
Comet MS/MS searches uninterpreted tandem mass spectra of peptides against sequence databases.
uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
(COmpressive Read-mapping Accelerator) a compressive-acceleration tool for NGS read mapping methods.
Crass is designed to identify and reconstruct CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set.
enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.
a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.
(Computational Radiology Kit) a collection of algorithms and image processing tools developed by the Computational Radiology Laboratory team.
a Workflow Management System geared towards scientific workflows.
CrossMap is a program for genome coordinates conversion between different genome assemblies.
controllable lossy compression of BAM/CRAM files.
a set of tools for manipulation of CSV/TSV files. It is convenient for rapid data investigation and integration into analysis pipelines.
redistributable software libraries to support CUDA applications for Linux.
Keywords:
Other
a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s).
a libre server and cloud storage browser for Mac and Windows with support for FTP, SFTP, WebDAV, Amazon S3, OpenStack Swift, Backblaze B2, Microsoft Azure & OneDrive, Google Drive and Dropbox.
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself. cython is installed as a module within python.
a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.
finds all significant local alignments between reads.
a toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
a toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing.
a flexible library for parallel computing in Python.
provides joint management of analysis code and data. This enables you to comprehensively track the exact state of any analysis inputs that produced your results — across the entire lifetime of a project, and across multiple datasets.
GNU datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files.
is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.
Keywords:
Utilities
dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set.
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, …
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.
a Bioconductor software package installed in R 3.2.2 that estimates variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
bax file decoder and data compressor.
a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
a suite of tools for use in genome assembly and consensus.
a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
(Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.
a whole genome simulator for next-generation sequencing based off of wgsim found in SAMtools, which was written by Heng Li, and forked from DNAA. It was modified to handle ABI SOLiD and Ion Torrent data, as well as various assumptions about aligners and positions of indels. Many new features have been subsequently added.
estimates haplotype phase either within a genotyped cohort or using a phased reference panel. Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new, very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas: a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm …
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.
a Bioconductor software package installed in R 3.2.2 for examining differential expression of replicated count data.
provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
(EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).
a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.
an extensible, customizable, free/libre text editor.
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
EMu is a relative abundance estimator for 16S genomic sequences
a FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. Starting from a VCF file and a set of phenotypes encoded using the Human Phenotype Ontology (HPO), it will annotate, filter and prioritize likely causative variants based on user-defined criteria such as a variant's predicted pathogenicity, frequency of occurrence in a population and also how closely the given phenotype matches …
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
(Fast and Accurate Multiple Sequence Aligner) implements an algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM).
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
FastME provides distance algorithms to infer phylogenies.
Fastool is a simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them. It makes use of the KSeq library (http://lh3lh3.users.sourceforge.net/kseq.shtml) for fast access to FastQ/A files.
is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
a quality control tool for high throughput sequence data.
fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.
allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
a fast, flexible, user-friendly, cluster-friendly QTL mapper.
infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million sequences in a reasonable amount of time and memory.
an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data.
a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
FDT is an Application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.
(Feature frequency profile) an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
A set of tools to analyze genomic data with a focus on Next Generation Sequencing
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
a tool for filtering long reads by quality.
(Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge …
fast and accurate de novo assembler for single molecule sequencing reads.
an efficient FASTQ manipulation suite.
Bayesian haplotype-based polymorphism discovery and genotyping.
a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
finds somatic fusion-genes in RNA-seq data.
a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing tools (e.g. lobSTR or hipSTR) is that it can handle repeats that are longer than the read length. GangSTR takes aligned reads (BAM) and a set of repeats in the reference genome as input and outputs a VCF file containing genotypes for each locus.
(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
tools and libraries for interacting with Google Cloud products and services.
(Genome-wide Complex Trait Analysis) a tool for genome-wide complex trait analysis with five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait …
a population genetics package that computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including confidence intervals for “neighborhood size”.
a free tool offered by Golden Helix that delivers stunning visualizations of your genomic data, enabling you to see what is occurring at each base pair in your samples.
a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).
compares and evaluates the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie), collapses (merges) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples), and classifies transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).
validates, filters, converts and performs various other operations on GFF files (use gffread -h to see the various usage options). Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs. Thus the gffread utility can be used to simply …
(Generalized FOLD) a generalized fold change for ranking differentially expressed genes from RNA-seq data. GFOLD is especially useful when no replicate is available. GFOLD generalizes the fold change by considering the posterior distribution of log fold change, such that each gene is assigned a reliable fold change. It overcomes the shortcoming of p-value that measures the significance of whether a gene is differentially expressed …
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.
(GNU-based Virus IDentification) a Python3 program for Gene Novelty Unit-based Virus Identification for SARS-CoV-2. It ranks CDS nucleotide sequences in a genome fna file based on the number of observed exact CDS nucleotide matches in a public or private database. It was created to type SARS-CoV-2 genomes using a whole genome multilocus sequence typing (wgMLST) approach.
a set of command line tools to manipulate multiple alignments. Implemented in Go language, Goalign aims to handle multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, through several basic commands. Each command may print result (an alignment, for example) in the standard output, and thus can be piped to the standard input of the next goalign command.
provides functions for working on alignments in fasta format.
goleft is a collection of bioinformatics tools written in go distributed together as a single binary under a liberal (MIT) license. Running the binary goleft will give a list of subcommands with a short description. Running any subcommand without arguments will give a full help for that command
a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using a declarative query language, in a parallel execution engine. It is very efficient in a wide range of use-cases, including genome wide batch analysis, range-queries, genomic table joins of variants and segments, filtering, aggregation etc.
a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language. The goal is to handle phylogenetic trees in Newick, Nexus and PhyloXML formats, through several basic commands. Each command may print result (a tree for example) in the standard output, and thus can be piped to the standard input of the next gotree command.
grabix leverages the fantastic BGZF library in samtools to provide random access into text files that have been compressed with bgzip. grabix creates it's own index (.gbi) of the bgzipped file. Once indexed, one can extract arbitrary lines from the file with the grab command. Or choose random lines with the, well, random command.
GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.
GraphMap2 update containins tuning of alignments specific for long RNA reads. GraphMap2 is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.
GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling). It combines variation graph representation of gene sets with an LSH indexing scheme to allow for fast classification of metagenomic reads. Subsequent hierarchical local alignment of classified reads against graph traversals facilitates accurate reconstruction of full-length gene sequences using a simple scoring scheme.
an ultra-fast sequence alignment algorithm for intra-species genome comparison.
a tool to sort genomic files according to a genomefile.
is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees.
a scalable machine learning and predictive analytics platform.
an open-source, general-purpose, Python-based data analysis library with additional data types and methods for working with genomic data.
Developed for the detection of subtle allelic imbalance events from next-generation sequencing data, hapLOHseq is a sequencing-based extension of hapLOH, which is a method for the detection of subtle allelic imbalance events from SNP array data. It is capable of identifying events of 10 mega-bases or greater occurring in as little as 16% of the sample using exome sequencing data (at 80x) and 4% …
an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines.
is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.
HiC alignment and classification pipeline.
(Haplotype inference and phasing for Short Tandem Repeats) a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data. HipSTR was specifically developed to deal with short tandem repeats (STRs) in genomic sequences in the hopes of obtaining more robust STR genotypes.
(Hierarchical Indexing for Spliced Alignment of Transcripts) a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). HISAT2 is a successor to both HISAT and TopHat2.
a tool specially designed to analyze histone modification ChIP-seq data produced from cancer genomes. HMCan corrects for the GC-content and copy number bias and then applies Hidden Markov Models to detect the signal from the corrected data. On simulated data, HMCan outperformed several commonly used tools developed to analyze histone modification data produced from genomes without copy number alterations.
is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
Hopla enables classic genomic single, duo, trio, etc., analysis, by studying a single (multisample) vcf-file, eventually generating interactive visualizations.
is an interactive process viewer.
a Python package that provides infrastructure to process data from high-throughput sequencing assays.
a C library for reading/writing high-throughput sequencing data.
(Histosketching Using Little Kmers) a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
(Hypothesis Testing using Phylogenies) an open-source software package for comparative sequence analysis using stochastic evolutionary models.
The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.
(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.
Keywords:
Utilities
a software suite to create, edit, compose, or convert bitmap images.
(IMmunogenetic SEQuence Analysis) is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobolin gene sequencing experiments. It derives immune repertoires from sequencing data in FASTA / FASTQ format.
a pipeline for processing inDrops sequencing data.
(INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.