Pinned Repositories
dashi
Python Dash visualization of OICR QC data
data_release
Scripts for releasing data generated at OICR to stakeholders
debarcer
Debarcer: A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes
djerba
Create cancer bioinformatics reports from metadata and workflow output
medips-tools
Scripts for cfMeDIP QC analysis
miso-lims
MISO: An open-source LIMS for NGS sequencing centres, now with detailed samples
robust-paper
Ten Simple Rules for Making Research Software More Robust. Manuscript is published at PLoS Computational Biology. Feedback is welcome!
sequenza
Workflow for Sequenza, cellularity and ploidy
shesmu
Decision-driven action launching system
vidarr
Analysis provenance tracking server
Genome Sequence Informatics's Repositories
oicr-gsi/djerba
Create cancer bioinformatics reports from metadata and workflow output
oicr-gsi/shesmu
Decision-driven action launching system
oicr-gsi/cfMedipsQc
cfMedipsQC workflow produces a set of metrics files for sequencing data generated in methylation profiling of circulating Free DNA.
oicr-gsi/variantEffectPredictor
Variant Effect Predictor Workflow
oicr-gsi/emSeqQc
Runs bwa-meth followed by bamqc and methyldackel
oicr-gsi/bwaMem
Workflow for BWA mem
oicr-gsi/crosscheckFingerprintsCollector
workflow to generate per library fingerprints for use in gatk CrosscheckFingerprints
oicr-gsi/delly
Delly workflow produces a set of vcf files with different types of structural variant calls
oicr-gsi/dimsum
QC Tracking dashboard
oicr-gsi/hrDetect
Workflow for the sigtools and HRdetect R packages
oicr-gsi/mutect2
Workflow to run Mutect2 (GATK4)
oicr-gsi/bwamem2
workflow for bwa-men2
oicr-gsi/dellyGermline
Call germline SVs using Delly
oicr-gsi/dragmap
A workflow to run Dragmap
oicr-gsi/hotspotFingerprintCollector
common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools
oicr-gsi/ichorCNA
workflow for estimating the fraction of tumour in cell-free DNA from sWGS
oicr-gsi/mavis
MAVIS workflow, annotation of structural variants
oicr-gsi/mrdetect
workflow to detect Minimal Residual disease with MRDetect
oicr-gsi/msisensor
msisensor-pro workflow
oicr-gsi/mutect2Consensus
The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.
oicr-gsi/nanoporeCoverageAnalysis
Workflow for nanopore coverage analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeMapping
Workflow for nanopore reads mapping, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeRunSVAnalysis
Workflow for running structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/nanoporeSVAll
Workflow for executing all task of nanopore filterfastq, nanopore mapping, nanopore coverage analysis, nanopore structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.
oicr-gsi/probeCoverageDistribution
Workflow to calculate probe coverage, calls bwaMem
oicr-gsi/purple
oicr-gsi/star
Workflow for STAR RNAseq aligner
oicr-gsi/t1k
oicr-gsi/tmbAnalysis
A workflow to align fastq reads, call variants, annotate and assess TMB
oicr-gsi/umiCollapse
umiCollapse workflow, generating umi deduplicated bam file and stats