GalaxyData intensive science for everyone.
Stars: ✭ 812 (+2700%)
UgeneUGENE is free open-source cross-platform bioinformatics software
Stars: ✭ 112 (+286.21%)
RushA cross-platform command-line tool for executing jobs in parallel
Stars: ✭ 421 (+1351.72%)
ClusterflowA pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
Stars: ✭ 85 (+193.1%)
BioconvertBioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Stars: ✭ 112 (+286.21%)
atroposAn NGS read trimming tool that is specific, sensitive, and speedy. (production)
Stars: ✭ 109 (+275.86%)
platonIdentification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Stars: ✭ 52 (+79.31%)
FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Stars: ✭ 966 (+3231.03%)
MigmapHTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Stars: ✭ 38 (+31.03%)
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Stars: ✭ 2,404 (+8189.66%)
ngs pipelineExome/Capture/RNASeq Pipeline Implementation using snakemake
Stars: ✭ 40 (+37.93%)
gencoreGenerate duplex/single consensus reads to reduce sequencing noises and remove duplications
Stars: ✭ 91 (+213.79%)
grape-nfAn automated RNA-seq pipeline using Nextflow
Stars: ✭ 30 (+3.45%)
IARC-nfList of IARC bioinformatics nextflow pipelines
Stars: ✭ 34 (+17.24%)
NgseasyDockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Stars: ✭ 80 (+175.86%)
sc2-illumina-pipelineBioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
Stars: ✭ 18 (-37.93%)
ManormA robust model for quantitative comparison of ChIP-Seq data sets.
Stars: ✭ 16 (-44.83%)
CookiecutterDEPRECIATED! Please use nf-core/tools instead
Stars: ✭ 18 (-37.93%)
FlowrRobust and efficient workflows using a simple language agnostic approach
Stars: ✭ 73 (+151.72%)
DeeptoolsTools to process and analyze deep sequencing data.
Stars: ✭ 448 (+1444.83%)
FgbioTools for working with genomic and high throughput sequencing data.
Stars: ✭ 166 (+472.41%)
AfterqcAutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Stars: ✭ 169 (+482.76%)
needlestackMulti-sample somatic variant caller
Stars: ✭ 45 (+55.17%)
Bedops🔬 BEDOPS: high-performance genomic feature operations
Stars: ✭ 215 (+641.38%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (+89.66%)
companionThis repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
Stars: ✭ 21 (-27.59%)
peppyProject metadata manager for PEPs in Python
Stars: ✭ 29 (+0%)
ngs-preprocessA pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
Stars: ✭ 22 (-24.14%)
SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Stars: ✭ 124 (+327.59%)
NglessNGLess: NGS with less work
Stars: ✭ 115 (+296.55%)
Rnaseq WorkflowA repository for setting up a RNAseq workflow
Stars: ✭ 170 (+486.21%)
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 (-10.34%)
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 (+24.14%)
JvarkitJava utilities for Bioinformatics
Stars: ✭ 313 (+979.31%)
ScdeR package for analyzing single-cell RNA-seq data
Stars: ✭ 147 (+406.9%)
ScipipeRobust, flexible and resource-efficient pipelines using Go and the commandline
Stars: ✭ 826 (+2748.28%)
Fusiondirect.jl(No maintenance) Detect gene fusion directly from raw fastq files
Stars: ✭ 23 (-20.69%)
HtslibC library for high-throughput sequencing data formats
Stars: ✭ 529 (+1724.14%)
SnsAnalysis pipelines for sequencing data
Stars: ✭ 43 (+48.28%)
GatkOfficial code repository for GATK versions 4 and up
Stars: ✭ 1,002 (+3355.17%)
NextflowA DSL for data-driven computational pipelines
Stars: ✭ 1,337 (+4510.34%)
bistroA library to build and execute typed scientific workflows
Stars: ✭ 43 (+48.28%)
OpenGene.jl(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Stars: ✭ 60 (+106.9%)
PHATPathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Stars: ✭ 17 (-41.38%)
SVCollectorMethod to optimally select samples for validation and resequencing
Stars: ✭ 20 (-31.03%)
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Stars: ✭ 64 (+120.69%)
HARRecognize one of six human activities such as standing, sitting, and walking using a Softmax Classifier trained on mobile phone sensor data.
Stars: ✭ 18 (-37.93%)
RcpiMolecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Stars: ✭ 22 (-24.14%)
virnetVirNet: A deep attention model for viral reads identification
Stars: ✭ 26 (-10.34%)
bacnetBACNET is a Java based platform to develop website for multi-omics analysis
Stars: ✭ 12 (-58.62%)
argparse2tooltransparently build CWL and Galaxy XML tool definitions for any script that uses argparse
Stars: ✭ 24 (-17.24%)
picardmetrics🚦 Run Picard on BAM files and collate 90 metrics into one file.
Stars: ✭ 38 (+31.03%)
echolocatoRAutomated statistical and functional fine-mapping pipeline with extensive API access to datasets.
Stars: ✭ 13 (-55.17%)
GenomeAnalysisModuleWelcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
Stars: ✭ 19 (-34.48%)
RNAseq titration resultsCross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Stars: ✭ 22 (-24.14%)
conda-env-builderBuild and maintain multiple custom conda environments all in once place.
Stars: ✭ 18 (-37.93%)