somalier by brentp

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

created at Aug. 7, 2018, 2:52 p.m.

11 +0

254 +1

35 +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

135 +2

35 +0

redun by insitro

Yet another redundant workflow engine

created at Nov. 4, 2021, 12:14 a.m.

15 +0

488 +2

37 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

created at Feb. 4, 2015, 9:24 a.m.

19 +0

296 +0

37 +0

bionode by bionode

Modular and universal bioinformatics

created at Jan. 23, 2014, 11:56 p.m.

36 +0

308 +0

39 +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

zindex by mattgodbolt

Create an index on a compressed text file

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

23 +0

613 -1

41 +0

cruzdb by brentp

python access to UCSC genomes database

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

17 +0

134 +0

41 +0

bakta by oschwengers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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

14 +0

393 +2

42 +0

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

201 +0

50 -1

AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

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

46 +0

410 +1

52 +0

vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

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

26 +0

348 +0

55 +0

bpipe by ssadedin

Bpipe - a tool for running and managing bioinformatics pipelines

created at Oct. 20, 2014, 4:31 a.m.

19 +0

223 +0

56 +0

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

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

18 +0

157 +2

60 +0

bioservices by cokelaer

Access to Biological Web Services from Python.

created at Aug. 28, 2014, 3:24 p.m.

18 +0

271 +0

61 +0

pileup.js by hammerlab

Interactive in-browser track viewer

created at Jan. 27, 2015, 8:36 p.m.

20 +0

273 +1

66 +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

353 +1

66 +0

sift by teamdfir

SIFT

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

74 +0

470 +0

66 +0

dalliance by dasmoth

Interactive web-based genome browser.

created at July 1, 2010, 6:29 p.m.

34 +0

226 +0

68 +0

poly by bebop

A Go package for engineering organisms.

created at May 29, 2020, 9 p.m.

12 +0

649 +0

68 +0