ngs
There are 632 repositories under ngs topic.
google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
broadinstitute/gatk
Official code repository for GATK versions 4 and up
galaxyproject/galaxy
Data intensive science for everyone.
samtools/htslib
C library for high-throughput sequencing data formats
deeptools/deepTools
Tools to process and analyze deep sequencing data.
flowhub-team/awesome-omics
A collection of awesome things regarding all omics.
lindenb/jvarkit
Java utilities for Bioinformatics
aidenlab/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
maxplanck-ie/snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
bioconvert/bioconvert
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
fulcrumgenomics/fgbio
Tools for working with genomic and high throughput sequencing data.
galaxyproject/training-material
A collection of Galaxy-related training material
samtools/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
sortmerna/sortmerna
SortMeRNA: next-generation sequence filtering and alignment tool
OpenGene/AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
ugeneunipro/ugene
UGENE is free open-source cross-platform bioinformatics software
lgmgeo/AnnotSV
Annotation and Ranking of Structural Variation
open2c/cooler
A cool place to store your Hi-C
hms-dbmi/scde
R package for analyzing single-cell RNA-seq data
OpenGene/MutScan
Detect and visualize target mutations by scanning FastQ files directly
vanheeringen-lab/seq2science
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
epam/cloud-pipeline
Cloud agnostic genomics analysis, scientific computation and storage platform
ngless-toolkit/ngless
NGLess: NGS with less work
sequana/sequana
Sequana: a set of Snakemake NGS pipelines
CRG-CNAG/CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
lucapinello/CRISPResso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
cbg-ethz/V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
zhanxw/rvtests
Rare variant test software for next generation sequencing data
indexofire/pathongs
Pathogen NGS Documentary
ablab/IsoQuant
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
ncbi/TPMCalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
jdidion/atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
OpenGene/fastv
An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
OpenGene/gencore
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
YaqiangCao/cLoops
Accurate and flexible loops calling tool for 3D genomic data.