danielecook/Awesome-Bioinformatics

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 May 1, 2024, 3:51 p.m.

C++

32 +0

476 -1

147 +0

GitHub

bcbio-nextgen by bcbio

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

updated at May 1, 2024, 4:02 p.m.

Python

87 +0

974 +1

357 +0

GitHub

sra-explorer by ewels

Web application to explore the Sequence Read Archive.

updated at May 1, 2024, 9:15 p.m.

HTML

9 +0

188 +0

27 +0

GitHub

wormtable by wormtable

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

updated at May 1, 2024, 10:03 p.m.

Python

6 +0

28 +1

5 +0

GitHub

bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

updated at May 1, 2024, 11:03 p.m.

C++

30 +0

621 +2

162 +0

GitHub

gridss by PapenfussLab

GRIDSS: the Genomic Rearrangement IDentification Software Suite

updated at May 2, 2024, 1:11 a.m.

Java

24 +0

244 +1

73 +0

GitHub

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 2, 2024, 4:42 a.m.

Python

159 -1

3,080 +3

695 +0

GitHub

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

updated at May 2, 2024, 10:31 a.m.

C

62 +0

1,313 +1

308 +1

GitHub

scipipe by scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

updated at May 2, 2024, 10:32 a.m.

Go

38 +0

1,053 -1

72 +0

GitHub

hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

updated at May 2, 2024, 11:58 a.m.

C++

29 +0

475 +3

78 +1

GitHub

Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

updated at May 2, 2024, 12:20 p.m.

C

28 +0

728 +2

160 +0

GitHub

fastx_toolkit by agordon

FASTA/FASTQ pre-processing programs

updated at May 2, 2024, 2:09 p.m.

C

18 +0

157 +2

60 +0

GitHub

igv by igvteam

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

updated at May 2, 2024, 2:22 p.m.

Java

50 +0

610 +1

377 +0

GitHub

somalier by brentp

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

updated at May 2, 2024, 2:45 p.m.

Nim

11 +0

254 +1

35 +0

GitHub

diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

updated at May 2, 2024, 5:29 p.m.

C++

36 -1

961 +3

170 +1

GitHub

AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

updated at May 2, 2024, 7:47 p.m.

Perl

46 +0

410 +1

52 +0

GitHub

samtools by samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

updated at May 3, 2024, 1:26 a.m.

C

100 -1

1,552 +3

570 +0

GitHub

rnaseq_tutorial by griffithlab

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

updated at May 3, 2024, 2:10 a.m.

R

184 +0

1,312 +2

616 +1

GitHub

pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

updated at May 3, 2024, 4:14 a.m.

Cython

48 +0

750 +1

270 +0

GitHub

seqkit by shenwei356

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

updated at May 3, 2024, 6:52 a.m.

Go

27 +0

1,207 +3

156 +0

GitHub