wdl by broadinstitute

Workflow Description Language - Specification and Implementations

created at Jan. 12, 2018, 6:20 p.m.

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26 +0

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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.

113 +0

957 +4

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awesome-pipeline by pditommaso

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

created at July 19, 2014, 3:48 p.m.

234 +0

5,904 +9

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zindex by mattgodbolt

Create an index on a compressed text file

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

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wormtable by wormtable

Write-once-read-many table for large datasets.

created at Oct. 27, 2012, 5:01 p.m.

6 +0

27 +0

5 +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.

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grabix by arq5x

a wee tool for random access into BGZF files.

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

6 +0

83 +0

12 +0

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

csvtk by shenwei356

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

created at April 3, 2016, 2:31 p.m.

25 +0

951 +2

84 +1

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

5,812 +4

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oneliners by stephenturner

Useful bash one-liners for bioinformatics.

created at Oct. 19, 2013, 11:33 a.m.

157 -1

1,800 +6

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hail by hail-is

Cloud-native genomic dataframes and batch computing

created at Oct. 27, 2015, 8:55 p.m.

55 +0

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biocaml by biocaml

OCaml Bioinformatics Library

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

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PHAT by chgibb

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

created at Oct. 11, 2016, 3:04 p.m.

4 +0

17 +0

2 +0

smof by incertae-sedis

Explore and analyze biological sequence data

created at April 27, 2014, 12:34 p.m.

3 +0

15 +0

2 +0

awesome-alternative-splicing by HussainAther

Alternative splicing resource

created at March 31, 2018, 1:16 a.m.

4 +0

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9 +0

mosdepth by brentp

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

created at Aug. 24, 2017, 4:32 p.m.

23 -1

653 +3

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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

delly by dellytools

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

created at Nov. 15, 2013, 8:51 a.m.

34 +0

399 +1

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bcbio-nextgen by bcbio

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

created at Feb. 6, 2013, 11:14 a.m.

87 +0

974 +1

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