ngs

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.

python bioinformatics ngs htslib

UpdatedFeb 13, 2025
Cython

deeptools /deepTools

Star704

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

UpdatedMar 7, 2025
Python

flowhub-team /awesome-omics

Star504

A collection of awesome things regarding all omics.

awesome genomics ngs protein omics single-cell ngs-pipeline wgs-analysis

UpdatedJan 23, 2024

lindenb /jvarkit

Star496

Java utilities for Bioinformatics

java science bioinformatics genomics biology ngs next-generation-sequencing

UpdatedMar 16, 2025
Java

aidenlab /juicer

Star433

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

bioinformatics genomics ngs hi-c 3d-genome 3d-genome-browser

UpdatedNov 22, 2024
Shell

maxplanck-ie /snakepipes

Star394

Customizable workflows based on snakemake and python for the analysis of NGS data

workflow rna-seq snakemake ngs hi-c chip-seq atac-seq bisulfite-sequencing

UpdatedMar 13, 2025
Python

bioconvert /bioconvert

Star377

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

bioinformatics conversion ngs sniffer sequence convertor phylogeny bam2sam sam2bam bam2cram bcf2vcf bigbed2bed cram2bam cram2sam embl2ena embl2fasta embl2genbank fasta2fastq genbank2embl genbank2fasta

UpdatedDec 1, 2023
Python

galaxyproject /training-material

Star327

A collection of Galaxy-related training material

training tutorial materials ngs metagenomics rnaseq proteomics chip-seq usegalaxy hacktoberfest

UpdatedMar 17, 2025
HTML

fulcrumgenomics /fgbio

Sponsor

Star324

Tools for working with genomic and high throughput sequencing data.

bioinformatics scala genomics ngs umi analyzing-genomic-data fgbio molecular-indexes

UpdatedMar 13, 2025
Scala

samtools /htsjdk

Star285

A Java API for high-throughput sequencing data (HTS) formats.

java genomics ngs sequencing sam vcf dna java-api fasta bam cram

UpdatedMar 13, 2025
Java

sortmerna /sortmerna

Star255

SortMeRNA: next-generation sequence filtering and alignment tool

python bioinformatics cpp ngs sequencing alignment metatranscriptomics

UpdatedJan 1, 2025
C++

lgmgeo /AnnotSV

Star246

Annotation and Ranking of Structural Variation

annotation genetics ngs ranking cnv sv priorization

UpdatedMar 6, 2025
Tcl

ugeneunipro /ugene

Star227

UGENE is free open-source cross-platform bioinformatics software

science workflow bioinformatics cross-platform pipeline cpp ngs sequencing qt5 dna msa ugene

UpdatedMar 13, 2025
C++

open2c /cooler

Star214

A cool place to store your Hi-C

python bioinformatics genomics ngs file-format contact-matrix hdf5 sparse hi-c cooler 3d-genome chromatin

UpdatedMar 10, 2025
Python

OpenGene /AfterQC

Star209

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

bioinformatics quality-control ngs sequencing overlap error trimming filtering fastq qc adapter-trimming

UpdatedMay 14, 2020
Python

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Here are 665 public repositories matching this topic...

google /deepvariant

OpenGene /fastp

broadinstitute /gatk

galaxyproject /galaxy

samtools /htslib

pysam-developers /pysam