SnakepipesCustomizable workflows based on snakemake and python for the analysis of NGS data
HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
AfterqcAutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data
FgbioTools for working with genomic and high throughput sequencing data.
ScdeR package for analyzing single-cell RNA-seq data
NglessNGLess: NGS with less work
UgeneUGENE is free open-source cross-platform bioinformatics software
BioconvertBioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
SequanaSequana: a set of Snakemake NGS pipelines
NgseasyDockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
TadbitTADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
BayestyperA method for variant graph genotyping based on exact alignment of k-mers
GatkOfficial code repository for GATK versions 4 and up
MigmapHTS-compatible wrapper for IgBlast V-(D)-J mapping tool
FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
NgsfEstimation of per-individual inbreeding coefficients under a probabilistic framework
TifTransposon Insertion Finder - Detection of new insertions in NGS data
Fusiondirect.jl(No maintenance) Detect gene fusion directly from raw fastq files
ManormA robust model for quantitative comparison of ChIP-Seq data sets.
NgsdistEstimation of pairwise distances under a probabilistic framework
GalaxyData intensive science for everyone.
HtslibC library for high-throughput sequencing data formats
DeeptoolsTools to process and analyze deep sequencing data.
JvarkitJava utilities for Bioinformatics
platonIdentification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
ctdna-pipelineA simplified pipeline for ctDNA sequencing data analysis
DNAscanDNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.
gencoreGenerate duplex/single consensus reads to reduce sequencing noises and remove duplications
peppyProject metadata manager for PEPs in Python
fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
OpenGene.jl(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
iSkyLIMSis an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
SVCollectorMethod to optimally select samples for validation and resequencing
catchA package for designing compact and comprehensive capture probe sets.
atroposAn NGS read trimming tool that is specific, sensitive, and speedy. (production)
CONSENTScalable long read self-correction and assembly polishing with multiple sequence alignment
MTBseq sourceMTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
rctlA set of command line tools based on R and JavaScript.
PHATPathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
readfqA simple tool to calculate reads number and total base count in FASTQ file
IsoQuantReference-based transcript discovery from long RNA read
IARC-nfList of IARC bioinformatics nextflow pipelines
ilusA handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
alignment-nfWhole Exome/Whole Genome Sequencing alignment pipeline
asapA scalable bacterial genome assembly, annotation and analysis pipeline
ngsLDCalculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
BWA-MEMEFaster BWA-MEM2 using learned-index
angsd-wrapperUtilities for analyzing next generation sequencing data.
IMPACT-PipelineFramework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
bio-dockers🐳 Bio-dockers: dockerized bioinformatic tools
myVCFmyVCF: a web-based platform for target and exome mutations data management
disqA library for manipulating bioinformatics sequencing formats in Apache Spark
ngs pipelineExome/Capture/RNASeq Pipeline Implementation using snakemake