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

gffutils by daler

GFF and GTF file manipulation and interconversion

created at Oct. 12, 2011, 1:48 p.m.

14 +0

267 +0

74 +0

biocaml by biocaml

OCaml Bioinformatics Library

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

15 +0

121 +0

21 +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

bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

created at May 10, 2012, 10:18 p.m.

15 +0

226 +0

83 +0

redun by insitro

Yet another redundant workflow engine

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

15 +0

488 +2

37 +0

SKESA by ncbi

SKESA assembler

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

17 +0

104 +0

16 +0

wgsim by lh3

Reads simulator

created at Jan. 22, 2011, 10:57 p.m.

17 +0

248 +0

89 +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

bioSyntax by bioSyntax

Syntax highlighting for computational biology

created at Dec. 5, 2017, 2:25 a.m.

17 +0

247 +0

30 +0

pybedtools by daler

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

created at May 14, 2010, 9:09 p.m.

17 +0

293 +0

104 +1

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

parasail by jeffdaily

Pairwise Sequence Alignment Library

created at May 21, 2015, 7:31 p.m.

18 +0

233 +0

34 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

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

19 +0

296 +0

37 +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

bedtools by arq5x

A powerful toolset for genome arithmetic.

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

20 +0

140 +1

87 +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

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

mummer by mummer4

Mummer alignment tool

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

20 +0

420 +1

108 +0