ngs pipelineExome/Capture/RNASeq Pipeline Implementation using snakemake
Stars: ✭ 40 (+300%)
rctlA set of command line tools based on R and JavaScript.
Stars: ✭ 15 (+50%)
IMPACT-PipelineFramework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Stars: ✭ 52 (+420%)
recentrifugeRecentrifuge: robust comparative analysis and contamination removal for metagenomics
Stars: ✭ 79 (+690%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (+450%)
CliqueSNVNo description or website provided.
Stars: ✭ 13 (+30%)
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.
Stars: ✭ 36 (+260%)
galaksioAn easy-to-use way for running Galaxy workflows.
Stars: ✭ 19 (+90%)
IARC-nfList of IARC bioinformatics nextflow pipelines
Stars: ✭ 34 (+240%)
BWA-MEMEFaster BWA-MEM2 using learned-index
Stars: ✭ 77 (+670%)
Training MaterialA collection of Galaxy-related training material
Stars: ✭ 184 (+1740%)
iSkyLIMSis an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
Stars: ✭ 33 (+230%)
myVCFmyVCF: a web-based platform for target and exome mutations data management
Stars: ✭ 18 (+80%)
platonIdentification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Stars: ✭ 52 (+420%)
ngs-preprocessA pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
Stars: ✭ 22 (+120%)
CONSENTScalable long read self-correction and assembly polishing with multiple sequence alignment
Stars: ✭ 47 (+370%)
Circle-MapA method for circular DNA detection based on probabilistic mapping of ultrashort reads
Stars: ✭ 45 (+350%)
GalaxyData intensive science for everyone.
Stars: ✭ 812 (+8020%)
ngs-in-biocA course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor
Stars: ✭ 37 (+270%)
readfqA simple tool to calculate reads number and total base count in FASTQ file
Stars: ✭ 19 (+90%)
rvtestsRare variant test software for next generation sequencing data
Stars: ✭ 114 (+1040%)
peppyProject metadata manager for PEPs in Python
Stars: ✭ 29 (+190%)
HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
Stars: ✭ 220 (+2100%)
ngsLDCalculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
Stars: ✭ 25 (+150%)
AfterqcAutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Stars: ✭ 169 (+1590%)
OpenGene.jl(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Stars: ✭ 60 (+500%)
angsd-wrapperUtilities for analyzing next generation sequencing data.
Stars: ✭ 13 (+30%)
JvarkitJava utilities for Bioinformatics
Stars: ✭ 313 (+3030%)
bio-dockers🐳 Bio-dockers: dockerized bioinformatic tools
Stars: ✭ 33 (+230%)
SVCollectorMethod to optimally select samples for validation and resequencing
Stars: ✭ 20 (+100%)
disqA library for manipulating bioinformatics sequencing formats in Apache Spark
Stars: ✭ 29 (+190%)
NgsdistEstimation of pairwise distances under a probabilistic framework
Stars: ✭ 6 (-40%)
needlestackMulti-sample somatic variant caller
Stars: ✭ 45 (+350%)
atroposAn NGS read trimming tool that is specific, sensitive, and speedy. (production)
Stars: ✭ 109 (+990%)
STingUltrafast sequence typing and gene detection from NGS raw reads
Stars: ✭ 15 (+50%)
ctdna-pipelineA simplified pipeline for ctDNA sequencing data analysis
Stars: ✭ 29 (+190%)
binMy bioinfo toolbox
Stars: ✭ 42 (+320%)
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.
Stars: ✭ 26 (+160%)
grape-nfAn automated RNA-seq pipeline using Nextflow
Stars: ✭ 30 (+200%)
Fusiondirect.jl(No maintenance) Detect gene fusion directly from raw fastq files
Stars: ✭ 23 (+130%)
rnftoolsRNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
Stars: ✭ 14 (+40%)
PHATPathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Stars: ✭ 17 (+70%)
JovianMetagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
Stars: ✭ 14 (+40%)
gencoreGenerate duplex/single consensus reads to reduce sequencing noises and remove duplications
Stars: ✭ 91 (+810%)
ngs-test-dataA workflow for creating small NGS test data sets, useful for continuous integration.
Stars: ✭ 19 (+90%)
IsoQuantReference-based transcript discovery from long RNA read
Stars: ✭ 26 (+160%)
MGSEMapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
Stars: ✭ 22 (+120%)
HtslibC library for high-throughput sequencing data formats
Stars: ✭ 529 (+5190%)
SnakepipesCustomizable workflows based on snakemake and python for the analysis of NGS data
Stars: ✭ 226 (+2160%)
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.
Stars: ✭ 64 (+540%)
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Stars: ✭ 2,404 (+23940%)
fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
Stars: ✭ 25 (+150%)
alignment-nfWhole Exome/Whole Genome Sequencing alignment pipeline
Stars: ✭ 19 (+90%)
TifTransposon Insertion Finder - Detection of new insertions in NGS data
Stars: ✭ 9 (-10%)
ManormA robust model for quantitative comparison of ChIP-Seq data sets.
Stars: ✭ 16 (+60%)
DeeptoolsTools to process and analyze deep sequencing data.
Stars: ✭ 448 (+4380%)
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Stars: ✭ 64 (+540%)
asapA scalable bacterial genome assembly, annotation and analysis pipeline
Stars: ✭ 47 (+370%)