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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.
(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.
AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.
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.
(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
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.
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.
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.
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.
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.
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.
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.
(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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
(EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
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.
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.
a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
scripts for estimating mutant fitness by sequencing randomly barcoded transposons (RB-TnSeq).
(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 …
(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.
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”.
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 …
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.
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
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 open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.
(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.
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
a Python package that provides infrastructure to process data from high-throughput sequencing assays.
a C library for reading/writing high-throughput sequencing data.
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).
(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.
an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble transcripts from RNA-Seq reads (in fasta format). Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting k-mers which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of …
a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can: Go from raw fastq files to Hi-C maps binned at many resolutions Automatically annotate loops and contact domains with the Juicer tools Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.
a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
implements a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particulary good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and …
KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. K-mer counting is important for many bioinformatics applications, e.g., developing de Bruijn graph assemblers. Building de Bruijn graphs is a commonly used approach for genome assembly with data from second-generation sequencer. Unfortunately, sequencing errors (frequent in practice) results in huge memory …
is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments.
is a tool for digital spoligotyping of MTB strains from Illumina read data.
(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites.
An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes.
a set of fast and accurate sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. This is done by using a reference set of full-length ribosomal RNA sequences for which known taxonomies are known, and for which a set of high quality OTU clusters has been previously generated. For each read, the best guess and corresponding confidence in …
(Mapping and Assembly with Qualities) builds mapping assemblies from short reads generated by the next-generation sequencing machines.
is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads.
(Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.
(Metagenomic Inquiry Compressive Acceleration) a family of programs for performing compressively-accelerated metagenomic sequence searches based on BLASTX and DIAMOND.
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to …
is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap …
whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).
(Mixture-of-Isoforms) for isoform quantitation using RNA-Seq is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. MISO is installed as a standalone program and as a module within python.
a project to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Includes accelerated versions of DOTUR and SONS and the functionality of a number of other popular tools.
aggregates results from bioinformatics analyses across many samples into a single report.
RNA modification detection using Nanopore raw reads with Deep One Class classification.
a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.
Oncofuse is a framework designed to estimate the oncogenic potential of de-novo discovered gene fusions. It uses several hallmark features and employs a bayesian classifier to provide the probability of a given gene fusion being a driver mutation.
(Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.
A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.
The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in mapped concordance, number of mapped bases, …
Phantompeakqualtools computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
(phasing and Allele Specific Expression from RNA-seq) performs haplotype phasing using read alignments in BAM format from both DNA and RNA based assays, and provides measures of haplotypic expression for RNA based assays.
a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.
Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection.
is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment.
The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages. Pysam is installed as a module within python.
a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.
a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
(QUAlity score Reduction at Terabyte scale) an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.
(QUality ASsessment Tool) evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length; NG50, where length of the reference genome is being covered; NA50 and NGA50, where aligned blocks instead of contigs are taken; misassemblies, misassembled and unaligned contigs or contigs bases; and genes and …
rapid sensitive and accurate read mapping via quasi-mapping.
is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.
enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms to provide very quick, accurate expression estimates using little memory and performs inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.
a high performance, highly parallel, robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Because of its efficiency, it is an important work horse running in many sequencing centres around the world today.
a fast, flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
is a single-cell gene expression profile annotation tool using reference datasets.
SeqBuster integrates multiple analyses modules in a unique platform offering a deep characterization of miRNA variants (isomiRs).
is a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.
SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.
a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files, which can also be optionally compressed by gzip.
SINA aligns nucleotide sequences to match a pre-existing MSA using a graph based alignment algorithm similar to PoA. The graph approach allows SINA to incorporate information from many reference sequences building without blurring highly variable regions. While pure NAST implementations depend highly on finding a good match in the reference database, SINA is able to align sequences relatively distant to references with good quality …
implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming. It is specially designed for processing next-generation sequencing (NGS) paired-end sequences.
genomic variant annotation and functional effect prediction toolbox.
SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering ribosomal RNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.
is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.
a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Starcode is a DNA sequence clustering software. Starcode clustering is based on all pairs search within a specified Levenshtein distance (allowing insertions and deletions), followed by a clustering algorithm: Message Passing, Spheres or Connected Components. Typically, a file containing a set of DNA sequences is passed as input, jointly with the desired clustering distance and algorihtm. Starcode returns the canonical sequence of the cluster, …
a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that …
comprises a suite of software programs for processing next-gen sequencing read data including

- Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can …
an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, …
a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.

Mozilla Public License 2.0 (MPL-2.0)
a fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
quantifies mRNA abundance directly from the alignments by parsing BAM files. The input parameters are the same GTF files used to generate the alignments, and one or multiple input BAM file(s) containing either single-end or paired-end sequencing reads. The TPMCalculator output is comprised of four files per sample reporting the TPM values and raw read counts for genes, transcripts, exons and introns respectively.
identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
a flexible read trimming tool for Illumina NGS data.
a software package comprised of three independent software modules (Inchworm, Chrysalis, and Butterfly) for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
implements a Bayesian framework for calling de novo mutations in trios for next-generation sequencing data.
a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.
a library for the analysis of RNA velocity.
a sequence assembler for very short reads.
a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
an alternative to the USEARCH tool developed by Robert C. Edgar (2010) for which the source code is not publicly available, VSEARCH is an open source, multithreaded 64-bit tool for processing and preparing metagenomics, genomics, and population genomics nucleotide sequence data. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact …
WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.
The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).
a software package for analyzing snapshots of developmental processes in scRNA-seq data.
xAtlas is a fast and retrainable small variant caller that has been developed at the Baylor College of Medicine Human Genome Sequencing Center.
is a simple and easy to use long read error-correction tool which can detect and remove chimeras.
discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
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