smoove by brentp

structural variant calling and genotyping with existing tools, but, smoothly.

updated at April 13, 2024, 8:06 p.m.

10 +0

219 +0

21 +0

octopus by luntergroup

Bayesian haplotype-based mutation calling

updated at April 13, 2024, 5:26 a.m.

19 +0

296 +0

37 +0

bedtools by arq5x

A powerful toolset for genome arithmetic.

updated at April 12, 2024, 10:03 a.m.

20 +0

139 +0

87 +0

samstat by TimoLassmann

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

updated at April 12, 2024, 3:15 a.m.

3 +0

23 +0

7 +0

wgsim by lh3

Reads simulator

updated at April 11, 2024, 5:08 p.m.

17 +0

248 +0

89 +0

tabix by samtools

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

updated at April 11, 2024, 6:37 a.m.

22 +0

91 +0

40 +0

biocaml by biocaml

OCaml Bioinformatics Library

updated at April 11, 2024, 5:57 a.m.

15 +0

121 +0

21 +0

pybedtools by daler

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

updated at April 11, 2024, 12:51 a.m.

17 +0

293 +0

103 +0

cyvcf2 by brentp

cython + htslib == fast VCF and BCF processing

updated at April 10, 2024, 2:11 p.m.

7 +0

357 +0

70 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

updated at April 10, 2024, 9:48 a.m.

31 +0

392 +0

199 +0

wormtable by wormtable

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

updated at April 5, 2024, 5:59 p.m.

6 +0

27 +0

5 +0

seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

updated at March 31, 2024, 9:30 p.m.

12 +0

108 +0

22 +0

seqware by SeqWare

This is the SeqWare Project's main repo.

updated at March 31, 2024, 2:12 p.m.

26 +0

28 +0

17 +0

squiggle by IQTLabs

📈 DNA Sequence Visualization for Humans

updated at March 27, 2024, 4:50 a.m.

6 +0

38 +0

8 +0

awesome-alternative-splicing by HussainAther

Alternative splicing resource

updated at March 26, 2024, 4:54 p.m.

4 +0

45 +0

9 +0

seqfu2 by telatin

seqfu - Sequece Fastx Utilities

updated at March 26, 2024, 2:39 p.m.

3 +0

101 +0

6 +0

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

updated at March 26, 2024, 9:55 a.m.

18 +0

155 +0

60 +0

AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

updated at March 26, 2024, 7:30 a.m.

20 +0

201 +0

51 +0

fastqp by mdshw5

Simple FASTQ quality assessment using Python

updated at March 25, 2024, 9:06 a.m.

6 +0

107 +0

14 +0

bacannot by fmalmeida

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

updated at March 23, 2024, 2:41 p.m.

4 +0

94 +0

9 +0