jbrowse by GMOD

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

created at Jan. 16, 2009, 11:30 a.m.

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biopython by biopython

Official git repository for Biopython (originally converted from CVS)

created at March 15, 2009, 9:09 p.m.

170 -1

4,160 +12

1,711 +2

biocaml by biocaml

OCaml Bioinformatics Library

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

15 +0

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bioperl-live by bioperl

Core BioPerl 1.x code

created at May 12, 2010, 5:13 p.m.

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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

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bamtools by pezmaster31

C++ API & command-line toolkit for working with BAM data

created at May 21, 2010, 7:35 p.m.

27 +0

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dalliance by dasmoth

Interactive web-based genome browser.

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

34 +0

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vcflib by vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

created at Sept. 22, 2010, 11:25 p.m.

39 +0

593 +1

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circos by vigsterkr

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

created at Oct. 13, 2010, 9:28 p.m.

9 +0

68 +0

32 +0

freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

created at Oct. 13, 2010, 9:34 p.m.

46 +0

744 +1

259 +1

seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

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

12 +0

108 +0

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Scribl by chmille4

HTML5 canvas genomic graphics library

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

4 +0

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bedtools by arq5x

A powerful toolset for genome arithmetic.

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

20 +0

139 +0

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bwa by lh3

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

created at Jan. 14, 2011, 1:36 a.m.

106 +0

1,443 +2

542 +2

wgsim by lh3

Reads simulator

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

17 +0

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RSEM by deweylab

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

created at Feb. 9, 2011, 5:30 a.m.

23 +0

395 +1

117 +0

csvkit by wireservice

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

created at April 1, 2011, 3 a.m.

131 +0

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gatk by broadgsa

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

created at June 28, 2011, 1:08 p.m.

68 +0

293 +0

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mergesam by DarwinAwardWinner

Automate common sam & bam conversions

created at Aug. 26, 2011, 2:19 p.m.

3 +0

6 +0

1 +0

cruzdb by brentp

python access to UCSC genomes database

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

17 +0

133 +0

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