bioinformatics-pipeline

There are 66 repositories under bioinformatics-pipeline topic.

scipipe / scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
scientific-workflows bioinformatics-pipeline workflow go dataflow pipeline cheminformatics bioinformatics fbp scipipe workflow-engine golang
Language:Go 1052
grailbio / reflow
A language and runtime for distributed, incremental data processing in the cloud
bioinformatics-pipeline scientific-computing language runtime data-science cloud-computing aws analysis-pipeline golang
Language:Go 954
bacalhau-project / bacalhau
Compute over Data framework for public, transparent, and optionally verifiable computation
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 615
pysradb
saketkc / pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
bioinformatics ncbi-sra ncbi-sra-archive sratoolkit bioinformatics-pipeline sra ena
Language:Python 296
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 296
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 295
flowhub-team / WholeGenomeSequencing-WGS
Whole Genome Sequencing analysis, WGS analysis
bioinfomatics bioinformatics-pipeline genome wes wgs whole-genome-sequencing
240
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 226
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 226
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 220
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 218
kundajelab / atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
atac-seq dnase-seq bioinformatics-pipeline
Language:Python 160
sanger-pathogens / ariba
Antimicrobial Resistance Identification By Assembly
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 154
nickjcroucher / gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 153
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 145
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 143
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 genomics bioinformatics-pipeline genome-annotation
Language:Python 131
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 129
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 125
RNAlysis
GuyTeichman / RNAlysis
RNA sequencing analysis software
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool gui-application rna-seq rna-seq-analysis rna-seq-pipeline rnaseq smallrna smallrna-seq transcriptomics
Language:Python 121
ShujiaHuang / ilus
A handy variant calling pipeline generator for whole-genome 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.
whole-genome-sequencing variant-calling bioinformatics bioinformatics-pipeline pipeline
Language:Python 109
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 106
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 101
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 100
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 91
mitoNGS / MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
bioinformatics-pipeline mtdna mt-variant mitochondrial-variants mtoolbox
Language:Python 84
biowdl / tasks
A collection of reusable WDL tasks. Category:Other
bioinformatics bioinformatics-pipeline tasks wdl wdl-tasks workflow
Language:WDL 82
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 77
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 77
algbio / ggcat
Compacted and colored de Bruijn graph construction and querying
bioinformatics bioinformatics-pipeline sequencing de-novo-assembly debruijn-graph genome-assembly rust
Language:Rust 68
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 61
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 58
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.
molecular-informatics chemistry machine-learning deep-learning cheminformatics biology quantum-chemistry docking protein alphafold protein-structure-prediction awesome-list bioinformatics bioinformatics-pipeline bioinformatics-analysis proteomics genomics genetics genome-alignment protein-structure
Language:Python 56
sanger-pathogens / assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Perl 53
sanger-pathogens / iva
de novo virus assembler of Illumina paired reads
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 52
sagnikbanerjee15 / Finder
A fully automated gene annotator from RNA-Seq expression data
gene-annotations rna-seq gtf finder protein-sequences changepoint-detection gene-models transcripts predict-genes bioinformatics bioinformatics-pipeline gene-annotation-pipeline genome-annotation
Language:Python 51