wtdbg2 by ruanjue

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

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

30 +0

514 +0

94 +0

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.

32 +0

506 +1

148 +0

sift by teamdfir

SIFT

created at Jan. 18, 2014, 7:20 p.m.

73 +0

494 +0

65 +0

biojs by biojs

🔬A library of JavaScript components to represent biological data

created at Aug. 2, 2013, 3:05 p.m.

68 +0

494 +2

120 +0

mummer by mummer4

Mummer alignment tool

created at July 23, 2015, 5:33 p.m.

21 +0

473 +1

108 +0

AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

created at Nov. 19, 2019, 9:35 a.m.

45 +0

472 +5

57 +1

jbrowse by GMOD

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

created at Jan. 16, 2009, 11:30 a.m.

52 +0

464 +0

199 +0

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

created at Sept. 12, 2013, 7:02 p.m.

9 +0

463 +2

75 +0

FastQC by s-andrews

A quality control analysis tool for high throughput sequencing data

created at Dec. 21, 2017, 11:48 a.m.

13 +0

459 +2

86 +0

bakta by oschwengers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

created at Jan. 15, 2020, 11:08 p.m.

14 +0

458 +2

56 +1

delly by dellytools

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

created at Nov. 15, 2013, 8:51 a.m.

34 +0

448 +2

138 +1

RSEM by deweylab

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

created at Feb. 9, 2011, 5:30 a.m.

22 +0

424 +3

118 +0

bamtools by pezmaster31

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

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

27 +0

420 +0

153 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

created at May 30, 2013, 7:33 p.m.

41 +0

415 +0

154 +0

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.

25 +0

414 +1

82 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

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

29 +0

407 +1

200 +0

pyensembl by openvax

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

created at April 14, 2014, 3:23 p.m.

22 +0

384 +0

67 +0

cyvcf2 by brentp

cython + htslib == fast VCF and BCF processing

created at Aug. 12, 2015, 2:30 p.m.

7 +0

383 +0

72 +0

vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

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

26 +0

367 +0

56 +0

lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

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

27 +0

316 +0

119 +0