prokka by tseemann

Rapid prokaryotic genome annotation

updated at June 7, 2024, 7:40 p.m.

47 +0

770 +3

218 -1

bwa by lh3

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

updated at June 7, 2024, 7:33 p.m.

107 +0

1,468 +4

547 +0

awesome-pipeline by pditommaso

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

updated at June 7, 2024, 5:25 p.m.

235 +0

5,977 +9

617 +0

cromwell by broadinstitute

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

updated at June 7, 2024, 4:58 p.m.

112 +0

965 +2

351 +1

spades by ablab

SPAdes Genome Assembler

updated at June 7, 2024, 2:48 p.m.

32 +0

699 +13

130 +0

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

updated at June 7, 2024, 1:23 p.m.

58 +0

911 +2

285 +1

cufflinks by cole-trapnell-lab

None

updated at June 7, 2024, 9:53 a.m.

36 +0

306 +3

115 +0

samtools by samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

updated at June 7, 2024, 9:33 a.m.

100 +0

1,572 +1

572 +0

canu by marbl

A single molecule sequence assembler for genomes large and small.

updated at June 7, 2024, 8:57 a.m.

54 +0

638 +4

176 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

updated at June 7, 2024, 6:46 a.m.

31 +0

395 +2

201 +1

FastQC by s-andrews

A quality control analysis tool for high throughput sequencing data

updated at June 7, 2024, 6:01 a.m.

13 +0

403 +2

80 +0

WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

updated at June 6, 2024, 11:15 p.m.

14 +0

154 +1

32 +0

sra-explorer by ewels

Web application to explore the Sequence Read Archive.

updated at June 6, 2024, 7:09 p.m.

9 +0

189 +2

27 +0

redun by insitro

Yet another redundant workflow engine

updated at June 6, 2024, 6:51 p.m.

15 +0

489 +0

40 +0

AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

updated at June 6, 2024, 3:09 p.m.

47 -1

426 +3

52 +0

sift by teamdfir

SIFT

updated at June 6, 2024, 1:47 p.m.

74 +0

474 +1

66 +0

wgsim by lh3

Reads simulator

updated at June 6, 2024, 12:44 p.m.

17 +0

252 +1

90 +1

bionode by bionode

Modular and universal bioinformatics

updated at June 6, 2024, 10:58 a.m.

36 +0

309 +1

39 +0

oneliners by stephenturner

Useful bash one-liners for bioinformatics.

updated at June 6, 2024, 10:57 a.m.

157 +0

1,810 +1

512 +0

seqfu2 by telatin

seqfu - Sequece Fastx Utilities

updated at June 6, 2024, 8:37 a.m.

3 +0

102 +0

7 +0