AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

created at Aug. 4, 2015, 2:08 p.m.

20 +0

207 +0

51 +0

sra-explorer by ewels

Web application to explore the Sequence Read Archive.

created at Sept. 19, 2014, 8:15 a.m.

9 +0

203 +0

29 +0

ruffus by cgat-developers

CGAT-ruffus is a lightweight python module for running computational pipelines

created at Jan. 6, 2013, 10:20 p.m.

11 +0

173 +0

34 +0

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

created at Nov. 8, 2013, 1:03 p.m.

16 +0

173 +3

60 +0

WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

created at June 13, 2021, 1:32 p.m.

15 +0

162 +0

37 +0

genozip by divonlan

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

created at Dec. 15, 2019, 5:23 a.m.

1 +0

161 +2

12 +0

GLnexus by dnanexus-rnd

Scalable gVCF merging and joint variant calling for population sequencing projects

created at April 8, 2015, 5:05 a.m.

15 +0

154 +0

39 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

created at Jan. 3, 2011, 2:43 a.m.

20 +0

140 +0

85 +0

cruzdb by brentp

python access to UCSC genomes database

created at Sept. 2, 2011, 3:36 p.m.

17 +0

135 +0

42 +0

biocaml by biocaml

OCaml Bioinformatics Library

created at March 22, 2010, 10:08 p.m.

15 +0

123 +0

21 +0

seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

created at Nov. 24, 2010, 12:48 a.m.

12 +0

113 +0

22 +0

SKESA by ncbi

SKESA assembler

created at July 11, 2018, 8:13 p.m.

17 +0

112 +0

19 +0

seqfu2 by telatin

seqfu - Sequece Fastx Utilities

created at Nov. 26, 2020, 3:50 p.m.

3 +0

112 +0

7 +0

fastqp by mdshw5

Simple FASTQ quality assessment using Python

created at Sept. 23, 2013, 8:01 p.m.

6 +0

109 +0

14 +0

bacannot by fmalmeida

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

created at Oct. 23, 2019, 5:51 p.m.

4 +0

99 +1

9 +0

BigDataScript by pcingola

BigDataScript: Scirpting language for big data

created at March 3, 2013, 6 p.m.

13 +0

92 +0

21 +0

tabix by samtools

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

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

22 +0

91 +0

40 +0

grabix by arq5x

a wee tool for random access into BGZF files.

created at May 22, 2012, 1:53 p.m.

5 +0

84 +0

12 +0

fujiplot by mkanai

Fuji plot—a circos representation of multiple GWAS results—

created at Feb. 10, 2018, 12:23 p.m.

3 +0

78 +0

19 +0

Scribl by chmille4

HTML5 canvas genomic graphics library

created at Dec. 12, 2010, 9:18 p.m.

4 +0

76 +0

14 +0