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

51 +0

MultiQC by MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

created at Aug. 4, 2015, 1:47 p.m.

36 +0

1,167 +4

579 +1

mummer by mummer4

Mummer alignment tool

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

20 -1

419 +4

108 +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

477 +2

147 +0

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

created at June 12, 2015, 9:42 p.m.

65 +0

708 +6

290 +2

gridss by PapenfussLab

GRIDSS: the Genomic Rearrangement IDentification Software Suite

created at June 11, 2015, 11 a.m.

24 +0

243 +1

73 +0

parasail by jeffdaily

Pairwise Sequence Alignment Library

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

18 +0

233 +1

34 +0

vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

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

26 +0

348 +2

55 +0

poapy by ljdursi

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

created at April 28, 2015, 9:38 p.m.

8 +0

68 +0

12 +0

cromwell by broadinstitute

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

created at April 17, 2015, 7:39 p.m.

112 -1

958 +1

349 +1

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

133 +1

35 +0

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

created at March 10, 2015, 11:19 p.m.

37 +0

958 +4

169 -1

easy_qsub by shenwei356

Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.

created at March 9, 2015, 9:40 a.m.

3 +0

28 +0

8 +0

scipipe by scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

created at March 7, 2015, 9:47 p.m.

38 +0

1,054 +0

72 +0

zindex by mattgodbolt

Create an index on a compressed text file

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

23 +0

614 +1

41 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

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

19 +0

296 +0

37 +0

pileup.js by hammerlab

Interactive in-browser track viewer

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

20 +0

272 +1

66 +0

rust-bio by rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

created at Jan. 25, 2015, 4:40 p.m.

70 +0

1,507 +11

199 +2

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

common-workflow-language by common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

created at Sept. 25, 2014, 11:04 a.m.

112 +0

1,441 +1

199 +0