Genome Sequence Informatics

All

249 repositories

shesmu
Public
Decision-driven action launching system
infrastructure bioinformatics bioinformatics-pipeline workflow-management workflow-launching
Java
•
MIT License
•5•9•0•2•Updated Aug 1, 2025Aug 1, 2025
vidarr
Public
Analysis provenance tracking server
infrastructure
Java
•
MIT License
•2•2•0•3•Updated Aug 1, 2025Aug 1, 2025
cardea
Public
Case data API
infrastructure
Java
•
Apache License 2.0
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
dimsum
Public
QC Tracking dashboard
infrastructure
Java
•
GNU General Public License v3.0
•0•1•0•2•Updated Aug 1, 2025Aug 1, 2025
freec
Public
freec workflow - call CNV on your tumor wih optional normal
workflow analysis variant-calling cnv
WDL
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
ncov2019ArticNf
Public
ncov2019ArticNf workflow executes the ncov2019-artic-nf Nextflow workflow from connor-lab (https://github.com/connor-lab/ncov2019-artic-nf).
workflow
WDL
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
probeCoverageDistribution
Public
Workflow to calculate probe coverage, calls bwaMem
workflow
WDL
•
GNU General Public License v2.0
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
purple
Public
workflow
WDL
•0•1•0•0•Updated Jul 31, 2025Jul 31, 2025
djerba
Public
Create cancer bioinformatics reports from metadata and workflow output
infrastructure interpretation djerba
Python
•
GNU General Public License v3.0
•7•11•10•2•Updated Jul 31, 2025Jul 31, 2025
Analysis_Reports
Public
for generation of analysis reports to accompany released data
tools release
Python
•0•0•0•1•Updated Jul 30, 2025Jul 30, 2025
rnaSeqQC
Public
RNASeqQC workflow
workflow
WDL
•
GNU General Public License v3.0
•1•1•0•1•Updated Jul 30, 2025Jul 30, 2025
rsem
Public
WDL workflow for RSEM tool (transcription analysis for RNAseq)
workflow expression rnaseq transcription
WDL
•
GNU General Public License v3.0
•2•0•0•1•Updated Jul 30, 2025Jul 30, 2025
sarsCoV2Analysis
Public
Classify samples as being either SARS-CoV-2 positive or negative, identify the strain of virus, and produce statistics about the mapping.
workflow bioinformatics-analysis bioinformatics-workflow covid-19 covid19
WDL
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
sequenza
Public
Workflow for Sequenza, cellularity and ploidy
workflow rnaseq cnv copy-number-variation cnv-detection cnv-analysis
R
•2•19•2•1•Updated Jul 30, 2025Jul 30, 2025
sexcmdWorkflow
Public
wdl wrapper for SEXCMD tool. Identification of donor's sex using fastq inputs
workflow
WDL
•
MIT License
•1•1•0•0•Updated Jul 30, 2025Jul 30, 2025
strelkaSomatic
Public
Strelka2 somatic variant calling workflow
workflow wdl variant-calling strelka wdl-workflow
WDL
•
GNU General Public License v3.0
•0•1•0•0•Updated Jul 30, 2025Jul 30, 2025
deepTumourWorkflow
Public
Workflow for DeepTumour
WDL
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
strelka
Public
Workflow to run Strelka1 for variant calling
workflow
WDL
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
sniffles
Public
Workflow to run Structural Variant caller for Nanopore
workflow
WDL
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
smallBamQc
Public
Generate BAM file metrics for OICR's QC Gates as fast as possible
workflow
WDL
•0•0•0•1•Updated Jul 30, 2025Jul 30, 2025
mrdetect
Public
workflow to detect Minimal Residual disease with MRDetect
workflow
WDL
•0•0•1•0•Updated Jul 30, 2025Jul 30, 2025
smmipsWorkflow
Public
Workflow for analysis of smMIP libraries
workflow
WDL
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MIT License
•0•0•0•1•Updated Jul 30, 2025Jul 30, 2025
starMulti
Public
workflow
WDL
•
GNU General Public License v3.0
•1•0•0•0•Updated Jul 30, 2025Jul 30, 2025
variantMerging
Public
a workflow for combining variant calls from SNV analyses done with different callers
workflow utility variant-analysis
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
variantEffectPredictor
Public
Variant Effect Predictor Workflow
workflow
WDL
•1•3•1•1•Updated Jul 29, 2025Jul 29, 2025
calculateContamination
Public
A WDL workflow that runs GATK4 CalculateContamination from FastQ files.
workflow
WDL
•0•0•0•0•Updated Jul 29, 2025Jul 29, 2025
umiConsensus
Public
Workflow to generate consensus sequence bases on UMIs using consensusCruncher.
workflow
WDL
•0•1•0•0•Updated Jul 29, 2025Jul 29, 2025
umiCollapse
Public
umiCollapse workflow, generating umi deduplicated bam file and stats
workflow
WDL
•0•0•0•0•Updated Jul 29, 2025Jul 29, 2025
crosscheckFingerprints
Public
workflow
WDL
•0•0•0•0•Updated Jul 29, 2025Jul 29, 2025
umiExtract
Public
workflow to extract UMI from fastq files and place in fastq header
workflow
WDL
•0•0•1•1•Updated Jul 29, 2025Jul 29, 2025