Top 75 ngs open source projects

Snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
Htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
Deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Training Material
A collection of Galaxy-related training material
Afterqc
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Fgbio
Tools for working with genomic and high throughput sequencing data.
Rna Seq Star Deseq2
RNA-seq workflow using STAR and DESeq2
Scde
R package for analyzing single-cell RNA-seq data
Ngless
NGLess: NGS with less work
Ugene
UGENE is free open-source cross-platform bioinformatics software
Bioconvert
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Sequana
Sequana: a set of Snakemake NGS pipelines
Ngseasy
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Tadbit
TADbit 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
Bayestyper
A method for variant graph genotyping based on exact alignment of k-mers
Abra2
ABRA2
✭ 65
javangsdna
Gatk
Official code repository for GATK versions 4 and up
Migmap
HTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Ngsf
Estimation of per-individual inbreeding coefficients under a probabilistic framework
✭ 10
cngs
Tif
Transposon Insertion Finder - Detection of new insertions in NGS data
✭ 9
perlngs
Fusiondirect.jl
(No maintenance) Detect gene fusion directly from raw fastq files
Manorm
A robust model for quantitative comparison of ChIP-Seq data sets.
Ngsdist
Estimation of pairwise distances under a probabilistic framework
✭ 6
ngs
Htslib
C library for high-throughput sequencing data formats
Deeptools
Tools to process and analyze deep sequencing data.
Jvarkit
Java utilities for Bioinformatics
platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
ctdna-pipeline
A simplified pipeline for ctDNA sequencing data analysis
DNAscan
DNAscan 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.
reg-gen
Regulatory 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
iSkyLIMS
is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
SVCollector
Method to optimally select samples for validation and resequencing
catch
A package for designing compact and comprehensive capture probe sets.
atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
CONSENT
Scalable long read self-correction and assembly polishing with multiple sequence alignment
MTBseq source
MTBseq 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.
rctl
A set of command line tools based on R and JavaScript.
readfq
A simple tool to calculate reads number and total base count in FASTQ file
✭ 19
ngsfastq
IsoQuant
Reference-based transcript discovery from long RNA read
IARC-nf
List of IARC bioinformatics nextflow pipelines
ilus
A 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.
fastq-and-furious
Efficient handling of FASTQ files from Python
asap
A scalable bacterial genome assembly, annotation and analysis pipeline
ngsLD
Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
bio-dockers
🐳 Bio-dockers: dockerized bioinformatic tools
myVCF
myVCF: a web-based platform for target and exome mutations data management
disq
A library for manipulating bioinformatics sequencing formats in Apache Spark
1-60 of 75 ngs projects