hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

updated at May 23, 2024, 1:39 p.m.

29 +0

486 +3

83 +1

deepvariant by google

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

updated at May 23, 2024, 1:24 p.m.

159 +0

3,097 +5

697 +1

vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

updated at May 23, 2024, 1:23 p.m.

26 +0

349 +1

56 +0

delly by dellytools

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

updated at May 23, 2024, 1:23 p.m.

34 +0

406 +3

136 +0

manta by Illumina

Structural variant and indel caller for mapped sequencing data

updated at May 23, 2024, 1:23 p.m.

41 +0

389 +1

151 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

updated at May 23, 2024, 8:02 a.m.

14 +0

270 +2

75 +0

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

updated at May 23, 2024, 7:48 a.m.

78 +0

842 +1

290 +0

bedtools2 by arq5x

bedtools - the swiss army knife for genome arithmetic

updated at May 23, 2024, 3:08 a.m.

58 +0

905 +1

285 +0

poly by bebop

A Go package for engineering organisms.

updated at May 23, 2024, 3:06 a.m.

12 +0

655 +1

68 +0

smoove by brentp

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

updated at May 23, 2024, 1:39 a.m.

10 +0

222 +1

21 +0

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.

updated at May 23, 2024, 12:34 a.m.

52 +1

458 +1

198 +1

bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

updated at May 22, 2024, 10:59 p.m.

15 +0

226 +0

85 +1

bakta by oschwengers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

updated at May 22, 2024, 4:17 p.m.

14 +0

402 +2

42 +0

pyensembl by openvax

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

updated at May 22, 2024, 12:31 p.m.

22 +0

354 +1

66 +0

bioperl-live by bioperl

Core BioPerl 1.x code

updated at May 22, 2024, 2:50 a.m.

54 +0

289 +1

178 +0

common-workflow-language by common-workflow-language

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

updated at May 22, 2024, 2:12 a.m.

112 +0

1,443 +2

199 +0

vcflib by vcflib

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

updated at May 21, 2024, 2:40 p.m.

39 +0

603 -1

219 +0

bcbio-nextgen by bcbio

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

updated at May 21, 2024, 1:58 p.m.

87 +0

978 +1

357 +0

canu by marbl

A single molecule sequence assembler for genomes large and small.

updated at May 21, 2024, 12:40 p.m.

54 +0

634 +2

176 -1

bacannot by fmalmeida

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

updated at May 21, 2024, 9:50 a.m.

4 +0

96 +1

9 +0