A Knowledge Base of BioDataBiomedical Data Analysis Workflows
A private knowledge base for you or your team, amongst a large public knowledge base, with code snippets.
Create a Team
A Marketplace of Workflows and Services
Buy premium workflows and/or free workflows with paid support from authors of workflows and software tools.
Become a Seller
A Discussion Forum to Exchange Ideas
Ask questions and exchange ideas on biomedical data analysis, potentially with a bounty.
Visit our Forum
Variant-calling pipeline for Restriction site-associated DNA sequencing
nf-core/radseq is a bioinformatics best-practice variant-calling pipeline for Restriction site-associated DNA sequencing (...
ENCODE pipeline for histone marks developed for the psychENCODE project
psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project.
The o...
Near-real time tracking of SARS-CoV-2 in Connecticut
Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
snakemake workflow to run cellranger on a given bucket using gke.
A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
ATLAS - Three commands to start analyzing your metagenome data
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
input:raw sequence reads
operation:Genome assembly
output:Annotation track
tool:checkm2
tool:prodigal
tool:snakemake-wrapper-utils
tool:MEGAHIT
tool:Atlas
tool:BBMap
tool:Biopython
tool:BioRuby
tool:Bwa-mem2
tool:cd-hit
tool:CheckM
tool:DAS
tool:Diamond
tool:eggNOG-mapper v2
tool:MetaBAT 2
tool:Minimap2
tool:MMseqs
tool:MultiQC
tool:Pandas
tool:Picard
tool:pyfastx
tool:SAMtools
tool:SemiBin
tool:Snakemake
tool:SPAdes
tool:SqueezeMeta
tool:TADpole
tool:VAMB
tool:CONCOCT
tool:gunc
tool:ete3
tool:gtdbtk
tool:h5py
tool:networkx
tool:numpy
tool:plotly
tool:psutil
tool:utils
topic:metagenomics
RNA-seq workflow using STAR and DESeq2
This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
input:raw sequence reads
operation:Gene expression profiling
output:ID list
tool:snakemake-wrapper-utils
tool:biomaRt
tool:PCAtools
tool:BiocParallel
tool:BWA
tool:Cutadapt
tool:DESeq2
tool:GFFutils
tool:MultiQC
tool:Pandas
tool:SAMtools
tool:Snakemake
tool:STAR
tool:cli
tool:stringr
tool:tidyverse
topic:RNA-Seq
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
format:VCF
input:raw sequence reads
operation:Variant calling
output:genetic variants
tool:gatk
tool:rust-bio-tools
tool:snakemake-wrapper-utils
tool:tabix
tool:BCFtools
tool:BWA
tool:FastQC
tool:MultiQC
tool:Pandas
tool:Picard
tool:SAMtools
tool:Snakemake
tool:Trimmomatic
tool:Variant Effect Predictor (VEP)
tool:common
tool:matplotlib
tool:numpy
tool:seaborn
topic:DNA
