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Projects in Awesome Lists tagged with bioinformatics-pipeline
A curated list of projects in awesome lists tagged with bioinformatics-pipeline .
https://github.com/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
Last synced: 19 Dec 2024
https://github.com/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
Last synced: 26 Oct 2024
https://github.com/bacalhau-project/bacalhau
Compute over Data framework for public, transparent, and optionally verifiable computation
ai-art ai-data-collection ai-pipeline batch-processing bioinformatics-pipeline data-analysis data-engineering data-science decentralized decentralized-computing distributed gene-sequencing insulators iot logging-framework orchestration-framework p2p video-processing
Last synced: 12 Nov 2024
https://github.com/saketkc/pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
bioinformatics bioinformatics-pipeline ena ncbi-sra ncbi-sra-archive sra sratoolkit
Last synced: 20 Dec 2024
https://github.com/sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 03 Nov 2024
https://github.com/r3fang/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing single-cell-analysis single-cell-atac-seq
Last synced: 16 Nov 2024
https://github.com/lynnlangit/gcp-for-bioinformatics
GCP for Bioinformatics Researchers
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-researchers gcp genomics google google-batch nextflow
Last synced: 18 Dec 2024
https://github.com/sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 03 Nov 2024
https://github.com/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.
atac-seq bioinformatics bioinformatics-pipeline chip-seq fastq ngs pipeline reproducible-research rna-seq snakemake sra workflows
Last synced: 19 Dec 2024
https://github.com/ngless-toolkit/ngless
NGLess: NGS with less work
bioinformatics bioinformatics-pipeline bwa fastq fastq-format genomics haskell haskell-language metagenomics next-generation-sequencing ngs samtools science
Last synced: 18 Dec 2024
https://github.com/cbg-ethz/v-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
biohackcovid20 biohackeu20 biohackeu21 biohackeu22 bioinformatics bioinformatics-pipeline conda genomics hiv ngs sars-cov-2 sarscov2 sequencing snakemake virus
Last synced: 22 Dec 2024
https://github.com/shujiahuang/ilus
A lightweight and 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.
bioinformatics bioinformatics-pipeline pipeline variant-calling whole-genome-sequencing workflow-management
Last synced: 17 Dec 2024
https://github.com/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
Last synced: 21 Nov 2024
https://gregoryschwartz.github.io/too-many-cells/
Cluster single cells and analyze cell clade relationships with colorful visualizations.
bioinformatics-algorithms bioinformatics-pipeline single-cell single-cell-analysis single-cell-rna-seq visualization
Last synced: 06 Nov 2024
https://github.com/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.
alternative-splicing bam-files bioinformatics-pipeline cell-cycle cell-type-classification clustering command-line-tool fastq-anaysis graphical-interface louvain-community-detection marker-gene-analysis network-analysis pagerank pathway-analysis python rna-seq-data scrna-seq-data single-cell-splicing splicing-quantification splicing-visualization
Last synced: 06 Nov 2024
https://github.com/chanzuckerberg/czid-web
Infectious Disease Sequencing Platform
bioinformatics bioinformatics-pipeline biology chan-zuckerberg-id computational-biology czid genomics global-health infectious-diseases metagenomic next-generation-sequencing research science sequencing virology
Last synced: 14 Nov 2024
https://github.com/jetbrains-research/snakecharm
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
bioinformatics-pipeline bioinformatics-tool intellij intellij-plugins pycharm python snakemake
Last synced: 17 Dec 2024
https://github.com/uc-bd2k/GREIN
GREIN : GEO RNA-seq Experiments Interactive Navigator
bioinformatics-analysis bioinformatics-pipeline gene-expression gene-expression-omnibus geo geo-data-processing graphical-interface grein interactive-analysis interactive-visualizations processing r rna-seq rna-seq-analysis rna-seq-data rna-seq-pipeline shiny-apps
Last synced: 13 Nov 2024
https://github.com/cihga39871/pipelines.jl
A lightweight and powerful Julia package for computational pipelines and workflows.
bioinformatics bioinformatics-pipeline computational-pipelines julia pipeline pipelines ruffus snakemake workflow workflows
Last synced: 19 Dec 2024
https://github.com/bobeobibo/phigaro
Phigaro is a scalable command-line tool for predicting phages and prophages
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool biological-data-analysis genomic-data-analysis genomic-regions genomics phage phages prophage
Last synced: 20 Nov 2024
https://github.com/databio/pypiper
Python toolkit for building restartable pipelines
bioinformatics bioinformatics-pipeline pipeline python python-toolkit
Last synced: 21 Dec 2024
https://github.com/conda-incubator/conda-env-builder
Build and maintain multiple custom conda environments all in one place.
bioinformatics bioinformatics-pipeline conda conda-environment scala
Last synced: 18 Nov 2024
https://github.com/cdcgov/seqsender
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
bioinformatics-pipeline biosample cdc cdc-influenza-division genbank gisaid gisaid-format gisaid-upload gisaid-uploader ncbi-biosamples ncbi-genbank ncbi-sra ncbi-submission ncird ncird-id seqsender sra
Last synced: 08 Nov 2024
https://github.com/Novartis/pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics
Last synced: 26 Sep 2024
https://github.com/hammerlab/biokepi
Bioinformatics Ketrew Pipelines
bioinformatics-ketrew-pipelines bioinformatics-pipeline ketrew ocaml
Last synced: 11 Nov 2024
https://github.com/mikedacre/fyrd
Submit functions and shell scripts to torque and slurm clusters or local machines using python.
bioinformatics-pipeline library python python2 python3 python3-library slurm slurm-cluster torque
Last synced: 02 Dec 2024
https://github.com/dvklopfenstein/reactomepy
Explore biomolecular pathways in Reactome from the command-line or a Python script
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool biological-networks biotech biotechnology molecular-biology pathway-analysis pathway-enrichment-analysis pathway-models protein-protein-interaction reactome reactome-pathway
Last synced: 28 Oct 2024
https://github.com/daylily-informatics/daylily
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
aws bioinformatics bioinformatics-pipeline budgeting cwl ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs
Last synced: 15 Nov 2024
https://github.com/biocontainers/workflows
Bioinformatics curated workflows that use Biocontainers tools
bioinformatics bioinformatics-pipeline workflows
Last synced: 14 Nov 2024
https://github.com/darwinawardwinner/cd4-csaw
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
bioconductor bioinformatics-pipeline chip-seq r reproducible-research rna-seq
Last synced: 08 Nov 2024
https://github.com/saketkc/riboraptor
Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)
bioinformatics bioinformatics-pipeline genomics riboseq ribosome-profiling snakemake
Last synced: 15 Oct 2024
https://github.com/mbhall88/streamformatics
Real-time species-typing visualisation for nanopore data.
bioinformatics bioinformatics-pipeline d3js japsa minimap2 nanopore nodejs
Last synced: 13 Oct 2024
https://github.com/deib-geco/pygmql
Python Library for data analysis based on GMQL
anaconda bedtools big-data binder bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool genomics gmql java jupyter-notebook pypi python scala
Last synced: 24 Nov 2024
https://github.com/pwwang/biopipen
A set of processes/pipelines for bioinformatics
bioinformatics bioinformatics-pipeline bioinformatics-scripts pipeline-framework
Last synced: 20 Dec 2024
https://github.com/sydney-informatics-hub/bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling
Last synced: 21 Nov 2024
https://github.com/sbg/tidycwl
Tidy Common Workflow Language Tools and Workflows
bioinformatics-pipeline common-workflow-language sevenbridges tidyverse
Last synced: 13 Nov 2024
https://github.com/rennelab/hybkit
Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.
bioinformatics bioinformatics-pipeline bioinformatics-tool clash genomics hyb qclash ribonomics
Last synced: 09 Oct 2024
https://github.com/lkremer/tecov
A pipeline to to determine the repeat content of genes and their neighboring regions.
bioinformatics-pipeline genome genomics repeatmasker transposable-elements
Last synced: 18 Nov 2024
https://github.com/dohlee/snakemake-hamburger
:snake::hamburger: A beginner's guide to modular snakemake workflows.
bioinformatics-pipeline reproducible-research snakemake snakemake-workflow
Last synced: 11 Nov 2024
https://github.com/fomightez/mini-pipelines
collection of scripts that chain together other scripts by preparing and processing/transforming data.
bash bioinformatics-pipeline pipelines pipelining python shell workflow-automation workflows
Last synced: 07 Nov 2024
https://github.com/soedinglab/transannot
TransAnnot - a fast transcriptome annotation pipeline
annotation assembly bioinformatics bioinformatics-pipeline transcriptomics
Last synced: 11 Nov 2024
https://github.com/cdcgov/nchhstp-dtbe-varpipe-wgs
This repository contains an analysis pipeline developed to characterize WGS output
bioinformatics bioinformatics-pipeline genomics pipeline variant-annotations variant-calling
Last synced: 08 Nov 2024
https://github.com/gersteinlab/texp
TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data
bioinformatics bioinformatics-pipeline
Last synced: 19 Nov 2024
https://github.com/pentalpha/r-peridot
Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.
bioconductor bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool differential-expression differential-expression-analysis gene-expression rna-seq-analysis rna-seq-pipeline
Last synced: 13 Nov 2024
https://github.com/dohlee/snakemake-gatk
:snake::wrench: Snakemake wrappers for GATK.
bioinformatics-analysis bioinformatics-pipeline gatk reproducible-research snakemake snakemake-workflows
Last synced: 11 Nov 2024
https://github.com/brainstorm/bwa-nextflow-benchmark
Small test to compare AWS and HPC on a very simple workflow
aws bioinformatics-pipeline bwa-mem hpc kubernetes nextflow samtools
Last synced: 15 Dec 2024
https://github.com/hernanmd/penncnv.illumina
Workflow for running PennCNV with Illumina platform final report
bash-script bioinformatics bioinformatics-pipeline cnv pharo pharo-smalltalk smalltalk
Last synced: 18 Dec 2024
https://github.com/fomightez/pdbsum-binder
Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics pandas pandas-dataframes protein-sequences protein-structure python snakemake
Last synced: 07 Nov 2024
https://github.com/dohlee/snakemake-cartesian-ddg
Snakemake pipeline for Rosetta 'cartesian-ddg' protocol for protein stability prediction upon mutations.
bioinformatics bioinformatics-pipeline protein protein-stability protein-structure rosetta
Last synced: 11 Nov 2024
https://github.com/cbg-ethz/scdna-pipe
Python data analysis pipeline for single cell copy number event history reconstruction
bioinformatics bioinformatics-pipeline data-analysis genomics python snakemake snakemake-workflows workflow
Last synced: 17 Nov 2024
https://github.com/hernanmd/penncnv.affy
Workflow for running PennCNV with Affymetrix platform files
bash-script bioinformatics bioinformatics-pipeline cnv shell-script
Last synced: 09 Nov 2024
https://github.com/czheluo/perl-script
Perl script for research
bioinformatics-pipeline perl-script
Last synced: 18 Nov 2024
https://github.com/ozankiratli/ngs-pipeline
A Bioinformatics pipeline to process Raw reads to VCF files in Bash
bash bioinformatics-pipeline raw-reads vcf
Last synced: 13 Nov 2024
https://github.com/czheluo/bioinformatics-tools
S (small) Bioinformatics Tools
Last synced: 18 Nov 2024
https://github.com/fomightez/pdbepisa-binder
Using data from PDBePISA with the convenience of Python and Jupyter.
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics nucleic-acids nucleic-sequence pandas pandas-dataframe protein-sequences protein-structure python snakemake
Last synced: 07 Nov 2024
https://github.com/gauravcodepro/genome-analysis-slurm-pbs
slurm and pbs scripts for genome, metagenome, transcriptome analysis.
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomic-data-analysis genomics genomics-visualization
Last synced: 09 Nov 2024
https://github.com/fomightez/tophat_and_bowtie
Tophat2 and Bowtie compatibility
bioinformatics bioinformatics-pipeline
Last synced: 07 Nov 2024
https://github.com/dfornika/simulate-genomes
Simulate genomic variation, based on input reference genomes
bioinformatics-pipeline data-simulation microbial-genomics
Last synced: 25 Nov 2024
https://github.com/pasted/targeted_sequencing_pipeline
Targeted sequencing pipeline for the Royal Devon & Exeter Molecular Genetics lab.
bioinformatics bioinformatics-pipeline
Last synced: 07 Nov 2024
https://github.com/lanl/edge2.x
EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
bioinformatics bioinformatics-pipeline
Last synced: 09 Dec 2024
https://github.com/pasted/simple_bash_pipeline
Historical version of targeted panel sequencing pipeline for Monogenic Diabetes. Originally developed as Masters in Bioinformatics project @ University of Exeter
bash bioinformatics-pipeline pipeline
Last synced: 07 Nov 2024
https://github.com/marcos-fernando/annotep_v1
AnnoTEP - a platform for the annotation of transposable elements in plants
bioinformatics bioinformatics-pipeline docker-image gui plants transposable-elements website
Last synced: 18 Dec 2024
https://github.com/jasonjiangs/rnaseq-chipseq-joint-pipeline
A easy configured and deployed pipeline for joint analysis with RNA-seq and ChIP-seq.
bioinformatics-pipeline chip-seq pipeline rna-seq
Last synced: 06 Nov 2024
https://github.com/gauravcodepro/plant-resistance_gene_isolator
I coded this function to make a comprehensive gene isolation for the plant resistance genes from the long reads sequencing. Given PacBio or Oxford Nanopore Reads, it will assemble, predict the plant disease resistance genes and will allow you to analyze the mutations in the plant disease resistance genes
bioinformatics bioinformatics-pipeline bioinformatics-tool fungal-effectors fungal-genomes plantdisease plantdiseasedetection plantgenomics planthealth
Last synced: 09 Nov 2024
https://github.com/fomightez/r_and_bioconductor
R and Bioconductor compatibility
bioinformatics bioinformatics-pipeline
Last synced: 07 Nov 2024
https://github.com/dohlee/snakemake-kallisto-sleuth
Kallisto-sleuth pipeline in snakemake.
bioinformatics bioinformatics-pipeline pipeline rna-seq rna-seq-analysis rna-seq-pipeline
Last synced: 11 Nov 2024
https://github.com/fomightez/bioinformatics_software_compatibility
Details of compatibility of software commonly used in tandem
bioinformatics bioinformatics-pipeline
Last synced: 07 Nov 2024
https://github.com/se7en69/rna-seq-data-processing-and-analysis-pipeline
This pipeline automates essential steps for RNA-Seq data analysis, including quality control, read trimming, alignment to a reference genome, and coverage quantification. It leverages tools like FastQC, fastp, STAR, and bedtools to ensure high-quality results, with MultiQC reports providing an overview at each stage.
bioinformaitcs-scripting bioinformatics bioinformatics-pipeline data-analysis linux scripts shell
Last synced: 18 Dec 2024
https://github.com/followthefourleafedclover/allen-mouse-brain-regional-marker-identifier
Find region specific markers within the Allen Institute for Brain Science: Mouse Whole Cortex and Hippocampus 10x Dataset
bioinformatics bioinformatics-pipeline pandas parquet python3 streamlit streamlit-webapp
Last synced: 08 Dec 2024
https://github.com/stjudecloud/rfcs
Request for Comments (RFCs) on the St. Jude Cloud Project.
bioinformatics bioinformatics-pipeline computational-biology cwl cwl-workflow discussion genomics proposal rfcs stjudecloud wdl wdl-workflow workflow workflow-engine
Last synced: 21 Nov 2024
https://github.com/npavlovikj/mlst_stringmlst_analyses
Scripts used to generate the analyses and figures in the paper "Systems-based approach for optimization of a scalable bacterial ST mapping assembly-free algorithm".
bioinformatics bioinformatics-pipeline mlst stringmlst
Last synced: 02 Dec 2024
