RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

updated at June 10, 2024, 2:57 a.m.

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846 -1

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mosdepth by brentp

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

updated at June 8, 2024, 6:34 p.m.

23 +0

667 +0

99 +0

seqan3 by seqan

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

updated at June 8, 2024, 2:07 p.m.

24 +0

390 +0

80 +0

cufflinks by cole-trapnell-lab

None

updated at June 7, 2024, 9:53 a.m.

36 +0

306 +0

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PyVCF by jamescasbon

A Variant Call Format reader for Python.

updated at June 7, 2024, 6:46 a.m.

31 +0

395 +0

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WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

updated at June 6, 2024, 11:15 p.m.

14 +0

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32 +0

wgsim by lh3

Reads simulator

updated at June 6, 2024, 12:44 p.m.

17 +0

252 +0

90 +0

seqfu2 by telatin

seqfu - Sequece Fastx Utilities

updated at June 6, 2024, 8:37 a.m.

3 +0

102 +0

7 +0

bioservices by cokelaer

Access to Biological Web Services from Python.

updated at June 4, 2024, 2:48 p.m.

18 +0

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poly by bebop

A Go package for engineering organisms.

updated at June 4, 2024, 9:11 a.m.

12 +0

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bcbio-nextgen by bcbio

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

updated at June 3, 2024, 9:29 p.m.

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979 +0

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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.

updated at June 3, 2024, 9:29 p.m.

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seqware by SeqWare

This is the SeqWare Project's main repo.

updated at June 3, 2024, 9:21 a.m.

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27 +0

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mummer by mummer4

Mummer alignment tool

updated at June 2, 2024, 3:18 p.m.

20 +0

426 +0

108 +0

gridss by PapenfussLab

GRIDSS: the Genomic Rearrangement IDentification Software Suite

updated at May 31, 2024, 3:39 a.m.

23 -1

245 +0

73 +0

pybedtools by daler

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

updated at May 30, 2024, 6:35 p.m.

16 -1

294 +0

104 +0

tabix by samtools

Note: tabix and bgzip binaries are now part of the HTSlib project.

updated at May 30, 2024, 1:14 a.m.

22 +0

92 +0

40 +0

common-workflow-language by common-workflow-language

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

updated at May 29, 2024, 11:38 a.m.

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1,445 +0

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vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

updated at May 29, 2024, 12:30 a.m.

26 +0

350 +0

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wtdbg2 by ruanjue

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

updated at May 28, 2024, 6:27 p.m.

31 +0

497 +0

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