bioinformatics-pipeline

There are 70 repositories under bioinformatics-pipeline topic.

scipipe / scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
bioinformatics bioinformatics-pipeline cheminformatics dataflow fbp go golang pipeline scientific-workflows scipipe workflow workflow-engine
Language:Go 1110
grailbio / reflow
A language and runtime for distributed, incremental data processing in the cloud
analysis-pipeline aws bioinformatics-pipeline cloud-computing data-science golang language runtime scientific-computing
Language:Go 972
bacalhau-project / bacalhau
Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.
p2p distributed iot bioinformatics-pipeline data-analysis data-engineering data-science decentralized video-processing batch-processing gene-sequencing logging-framework orchestration-framework insulators decentralized-computing ai-art ai-data-collection ai-pipeline
Language:Go 835
sanger-pathogens / Roary
Rapid large-scale prokaryote pan genome analysis
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Perl 356
pysradb
saketkc / pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
bioinformatics bioinformatics-pipeline ena ncbi-sra ncbi-sra-archive sra sratoolkit
Language:Python 345
r3fang / SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
single-cell-atac-seq single-cell-analysis bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing
Language:R 320
gcp-for-bioinformatics
lynnlangit / gcp-for-bioinformatics
GCP for Bioinformatics Researchers
gcp bioinformatics bioinformatics-pipeline bioinformatics-analysis genomics bioinformatics-researchers google nextflow google-batch
Language:Jupyter Notebook 279
sanger-pathogens / snp-sites
Finds SNP sites from a multi-FASTA alignment file
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:C 268
sanger-pathogens / Artemis
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Java 258
sanger-pathogens / circlator
A tool to circularize genome assemblies
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 248
flowhub-team / WholeGenomeSequencing-WGS
Whole Genome Sequencing analysis, WGS analysis
bioinfomatics bioinformatics-pipeline genome wes wgs whole-genome-sequencing
245
nickjcroucher / gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Language:Python 206
TOGA
hillerlab / TOGA
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
bioinformatics bioinformatics-pipeline genome-annotation genomics
Language:Python 196
sanger-pathogens / ariba
Antimicrobial Resistance Identification By Assembly
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 181
kundajelab / atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
atac-seq dnase-seq bioinformatics-pipeline
Language:Python 166
seq2science
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.
snakemake bioinformatics bioinformatics-pipeline atac-seq rna-seq chip-seq reproducible-research ngs pipeline sra workflows fastq
Language:Python 165
ngless-toolkit / ngless
NGLess: NGS with less work
haskell bioinformatics bioinformatics-pipeline samtools bwa next-generation-sequencing fastq-format fastq science ngs metagenomics genomics haskell-language
Language:Haskell 150
yupenghe / methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
bioinformatics-pipeline epigenetics dna-methylation nome-seq functional-genomics differential-methylation nome-seq-data calling-dmrs
Language:Python 145
V-pipe
cbg-ethz / V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
ngs snakemake conda biohackeu20 virus sequencing bioinformatics bioinformatics-pipeline biohackcovid20 sars-cov-2 sarscov2 hiv genomics biohackeu21 biohackeu22
Language:Jupyter Notebook 141
ShujiaHuang / ilus
A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.
whole-genome-sequencing variant-calling bioinformatics bioinformatics-pipeline pipeline workflow-management
Language:Python 140
RNAlysis
GuyTeichman / RNAlysis
Analyze your RNA sequencing data without writing a single line of code
rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna smallrna-seq gui-application
Language:Python 139
KarchinLab / open-cravat
A modular annotation tool for genomic variants
variant-annotations variant-annotation variant-analysis genomics genomic-data-analysis bioinformatics bioinformatics-pipeline bioinformatics-tool annotation-tool python python3 javascript
Language:JavaScript 136
GregorySchwartz / too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
single-cell visualization single-cell-analysis single-cell-rna-seq bioinformatics-pipeline bioinformatics-algorithms
Language:Haskell 114
nsalomonis / altanalyze
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
rna-seq-data alternative-splicing scrna-seq-data bioinformatics-pipeline clustering pathway-analysis network-analysis splicing-quantification splicing-visualization python fastq-anaysis bam-files single-cell-splicing cell-cycle cell-type-classification marker-gene-analysis graphical-interface command-line-tool pagerank louvain-community-detection
Language:Python 105
MaayanLab / Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
bioinformatics-pipeline jupyter-notebook notebook pipeline rna-seq rna-seq-analysis
Language:Jupyter Notebook 103
stjude-rust-labs / sprocket
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
bioinformatics bioinformatics-pipeline wdl wdl-devtools wdl-workflow workflow workflow-engine
Language:Rust 97
mitoNGS / MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
bioinformatics-pipeline mitochondrial-variants mt-variant mtdna mtoolbox
Language:Python 96
biowdl / tasks
A collection of reusable WDL tasks. Category:Other
bioinformatics bioinformatics-pipeline tasks wdl wdl-tasks workflow
Language:WDL 88
chanzuckerberg / czid-web
Infectious Disease Sequencing Platform
infectious-diseases genomics sequencing metagenomic science next-generation-sequencing research biology virology bioinformatics bioinformatics-pipeline computational-biology global-health czid chan-zuckerberg-id
Language:TypeScript 86
algbio / ggcat
Compacted and colored de Bruijn graph construction and querying
bioinformatics bioinformatics-pipeline de-novo-assembly debruijn-graph genome-assembly rust sequencing
Language:Rust 84
urmi-21 / pyrpipe
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
rna-seq rna-seq-pipeline ncbi-sra bioinformatics bioinformatics-pipeline bioinformatics-analysis python rna-seq-workflows conda bioconda
Language:Python 84
twoXes / awesome-structural-bioinformatics
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
alphafold awesome-list bioinformatics bioinformatics-analysis bioinformatics-pipeline biology cheminformatics chemistry deep-learning docking genetics genome-alignment genomics machine-learning molecular-informatics protein protein-structure protein-structure-prediction proteomics quantum-chemistry
Language:Python 74
YichaoOU / HemTools
HemTools: a collection of NGS pipelines and bioinformatic analyses
ngs ngs-analysis python r hpc-applications bioinformatics-pipeline bash data-visualization
Language:Python 73
AuReMe / metage2metabo
From annotated genomes to metabolic screening in large scale microbiotas
bioinformatics bioinformatics-pipeline metabolic-models
Language:Jupyter Notebook 64
JetBrains-Research / snakecharm
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
snakemake pycharm intellij-plugins python intellij bioinformatics-pipeline bioinformatics-tool
Language:Python 62
sagnikbanerjee15 / Finder
A fully automated gene annotator from RNA-Seq expression data
bioinformatics bioinformatics-pipeline changepoint-detection finder gene-annotation-pipeline gene-annotations gene-models genome-annotation gtf predict-genes protein-sequences rna-seq transcripts
Language:Python 60