vcftools by vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

created at June 25, 2015, 1:48 p.m.

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spades by ablab

SPAdes Genome Assembler

created at June 1, 2016, 3:06 p.m.

32 +0

683 +6

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wtdbg2 by ruanjue

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

created at Sept. 29, 2017, 10:24 a.m.

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PyVCF by jamescasbon

A Variant Call Format reader for Python.

created at Oct. 30, 2011, 4:52 p.m.

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MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

created at July 20, 2016, 6:17 a.m.

31 +0

1,275 +4

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bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

created at Dec. 20, 2012, 7:25 p.m.

30 +0

627 +4

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hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

created at May 9, 2019, 7:34 p.m.

29 +0

486 +3

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Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

created at March 17, 2016, 10:47 p.m.

28 +0

735 +4

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lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

created at Oct. 8, 2012, 9:09 a.m.

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seqkit by shenwei356

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

created at Feb. 28, 2016, 10:04 a.m.

27 +0

1,218 +3

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bamtools by pezmaster31

C++ API & command-line toolkit for working with BAM data

created at May 21, 2010, 7:35 p.m.

27 +0

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vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

created at April 29, 2015, 4 p.m.

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seqware by SeqWare

This is the SeqWare Project's main repo.

created at May 11, 2012, 3:51 p.m.

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csvtk by shenwei356

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

created at April 3, 2016, 2:31 p.m.

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SnpEff by pcingola

None

created at Jan. 31, 2014, 10:22 p.m.

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seqan3 by seqan

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

created at April 4, 2016, 12:39 p.m.

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gridss by PapenfussLab

GRIDSS: the Genomic Rearrangement IDentification Software Suite

created at June 11, 2015, 11 a.m.

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mosdepth by brentp

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

created at Aug. 24, 2017, 4:32 p.m.

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zindex by mattgodbolt

Create an index on a compressed text file

created at Feb. 26, 2015, 1:33 p.m.

23 +0

612 +0

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tabix by samtools

Note: tabix and bgzip binaries are now part of the HTSlib project.

created at March 9, 2012, 1:46 a.m.

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