Sep 30 2019
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pbalign
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.
Updated versions:
0.4.1 | Linux 64
0.4.1 | OS X INTEL
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Sep 30 2019
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pbmm2
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, and especially runtime. pbmm2 is the official replacement for BLASR.
Updated versions:
1.1.0 | OS X INTEL
1.1.0 | Linux 64
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Sep 28 2019
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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.
Updated versions:
5.3.3 | OS X INTEL
5.3.3 | Linux 64
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Sep 27 2019
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pbbam
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.
Updated versions:
1.0.6 | Linux 64
1.0.6 | OS X INTEL
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Sep 27 2019
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KMC
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 requirements for de Bruijn graphs, as well as long build time. One of the popular approaches to handle this problem is filtering the input reads in such a way that unique k-mers (very likely obtained as a result of an error) are discarded.
Updated versions:
3.0.0 | OS X INTEL
3.0.0 | Linux 64
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Sep 27 2019
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miniasm
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 the raw input reads.
Updated versions:
0.3_r179 | OS X INTEL
0.3_r179 | Linux 64
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Sep 27 2019
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preseq
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.
Updated versions:
2.0.3 | Linux 64
2.0.3 | OS X INTEL
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Sep 26 2019
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VarScan
a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.
Updated versions:
2.4.4 | Linux 64
2.4.4 | OS X INTEL
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Sep 26 2019
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R
a free software environment for statistical computing and graphics.
Updated versions:
3.5.1 | Linux 64
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Sep 26 2019
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bcbio-variation-recall
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.
Updated versions:
0.2.6 | OS X INTEL
0.2.6 | Linux 64
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Sep 26 2019
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bcbio-prioritize
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.
Updated versions:
0.0.8 | Linux 64
0.0.8 | OS X INTEL
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Sep 25 2019
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crass
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.
Updated versions:
1.0.1 | OS X INTEL
1.0.1 | Linux 64
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Sep 24 2019
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OpenJDK
(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).
Updated versions:
zulu12.3.11-ca-jdk12.0.2-linux_x64 | Linux 64
zulu12.3.11-ca-jdk12.0.2-macosx_x64 | OS X INTEL
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Sep 24 2019
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MinCED
MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes.
Updated versions:
0.4.2 | Linux 64
0.4.2 | OS X INTEL
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Sep 24 2019
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dDocent
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.
Updated versions:
2.7.8 | OS X INTEL
2.7.8 | Linux 64
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Sep 23 2019
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grabix
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.
Updated versions:
0.1.8 | Linux 64
0.1.8 | OS X INTEL
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Sep 23 2019
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CRISPRCasFinder
a tool that 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.
Updated versions:
4.2.19 | Linux 64
4.2.19 | OS X INTEL
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Sep 23 2019
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csvtk
a set of tools for manipulation of CSV/TSV files. It is convenient for rapid data investigation and integration into analysis pipelines.
Updated versions:
0.18.2 | Linux 64
0.18.2 | OS X INTEL
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Sep 22 2019
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bmtool
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets.
Updated versions:
3.101 | OS X INTEL
3.101 | Linux 64
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Sep 22 2019
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Exonerate
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.
Updated versions:
2.4.0 | Linux 64
2.4.0 | OS X INTEL
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Sep 22 2019
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PAML
A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
Updated versions:
4.9 | OS X INTEL
4.9 | Linux 64
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Sep 21 2019
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GraphMap2
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.
Updated versions:
0.6.1 | Linux 64
0.6.1 | OS X INTEL
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Sep 21 2019
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GraphMap
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.
Updated versions:
0.5.2 | Linux 64
0.5.2 | OS X INTEL
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Sep 21 2019
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minialign
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.
Updated versions:
0.6.0 | OS X INTEL
0.6.0 | Linux 64
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Sep 21 2019
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BEDOPS
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.
Updated versions:
2.4.36 | Linux 64
2.4.36 | OS X INTEL
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Sep 21 2019
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vt
A tool set for short variant discovery in genetic sequence data.
Updated versions:
0.57721 | OS X INTEL
0.57721 | Linux 64
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Sep 20 2019
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SINA
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 and will yield a robust result for query sequences with many close reference.
Updated versions:
1.6.0 | OS X INTEL
1.6.0 | Linux 64
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Sep 20 2019
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SortMeRNA
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).
Updated versions:
2.1b | OS X INTEL
2.1b | Linux 64
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Sep 20 2019
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goleft
goleft is a collection of bioinformatics tools written in go distributed together as a single binary.
Updated versions:
0.2.1 | Linux 64
0.2.1 | OS X INTEL
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Sep 20 2019
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Starcode
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, the cluster size, the set of different sequences that compose the cluster and the input line numbers of the cluster components.
Updated versions:
1.3 | OS X INTEL
1.3 | Linux 64
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Sep 20 2019
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MethylDackel
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.
Updated versions:
0.4.0 | Linux 64
0.4.0 | OS X INTEL
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Sep 20 2019
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WiggleTools
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).
Updated versions:
1.2.3 | OS X INTEL
1.2.3 | Linux 64
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Sep 19 2019
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xAtlas
xAtlas is a fast and retrainable small variant caller that has been developed at the Baylor College of Medicine Human Genome Sequencing Center.
Updated versions:
0.1 | OS X INTEL
0.2.1 | Linux 64
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Sep 19 2019
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Octopus
Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.
Updated versions:
0.5.2b | OS X INTEL
0.5.2b | Linux 64
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Sep 19 2019
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BAMscale
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.
Updated versions:
0.0.5 | OS X INTEL
0.0.5 | Linux 64
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Sep 19 2019
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bedtools
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 can be conducted by combining multiple bedtools operations on the UNIX command line.
Updated versions:
2.29.0 | OS X INTEL
2.29.0 | Linux 64
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Sep 18 2019
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BUStools
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.
Updated versions:
0.39.3 | Linux 64
0.39.3 | OS X INTEL
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Sep 18 2019
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AlignStats
AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.
Updated versions:
0.8 | OS X INTEL
0.8 | Linux 64
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Sep 18 2019
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DIAMOND
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.
Updated versions:
0.9.26 | Linux 64
0.9.26 | OS X INTEL
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Sep 17 2019
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PHESANT
PHESANT - PHEnome Scan ANalysis Tool
Run a phenome scan (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank.
There are three components in this project:
Running a phenome scan in UK Biobank
Post-processing of results
PHESANT-viz: Visualising the results
Updated versions:
0.18 | Linux 64
0.18 | OS X INTEL
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Sep 17 2019
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ARAGORN
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.
Updated versions:
1.2.38 | Linux 64
1.2.38 | OS X INTEL
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Sep 17 2019
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SeqPrep
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.
Updated versions:
1.3.2 | Linux 64
1.3.2 | OS X INTEL
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Sep 17 2019
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Bowtie
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
Updated versions:
1.2.1.1 | OS X INTEL
1.2.3 | OS X INTEL
1.2.3 | Linux 64
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Sep 16 2019
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SMALT
SMALT aligns DNA sequencing reads with a reference genome.
Reads from a wide range of sequencing platforms can be processed, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads are supported. There is no support for SOLiD reads.
Updated versions:
0.7.6 | OS X INTEL
0.7.6 | Linux 64
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Sep 16 2019
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STAR
(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Updated versions:
2.7.2b | OS X INTEL
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Sep 13 2019
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Vmatch
a versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements.
Updated versions:
2.3.0 | Linux 64
2.3.0 | OS X INTEL
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Sep 13 2019
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MacSyFinder
a program to model and detect macromolecular systems, genetic pathways in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features and to allow their efficient detection.
Updated versions:
1.0.5 | Linux 64
1.0.5 | OS X INTEL
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Sep 06 2019
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CNVkit
a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
Updated versions:
0.9.6 | Linux 64
0.9.6 | OS X INTEL
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