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/sequenza
Workflow for Sequenza, cellularity and ploidy
oicr-gsi/hlaminer
wrapper workflow for BCGSC tool HLAminer
oicr-gsi/rnaSeqQC
RNASeqQC workflow
oicr-gsi/sexcmdWorkflow
wdl wrapper for SEXCMD tool. Identification of donor's sex using fastq inputs
oicr-gsi/strelkaSomatic
Strelka2 somatic variant calling workflow
oicr-gsi/umiConsensus
Workflow to generate consensus sequence bases on UMIs using consensusCruncher.
oicr-gsi/determinePhiX
Workflow to determine PhiX contamination of undetermined reads
oicr-gsi/sarsCoV2Analysis
Classify samples as being either SARS-CoV-2 positive or negative, identify the strain of virus, and produce statistics about the mapping.
oicr-gsi/callability
oicr-gsi/cuplr
oicr-gsi/empty
Empty workflow for testing infrastructure
oicr-gsi/fastqc
Workflow for FastQC
oicr-gsi/hlavbseq
workflow wraps HLA-VBSeq, a tool for estimating the most prevalent HLA types in a sample
oicr-gsi/immunedeconvWorkflow
Workflow to run immunedeconv functions
oicr-gsi/InsertSizeMetrics
Workflow to run picard InsertSizeMetrics
oicr-gsi/manta
MantaSV workflow
oicr-gsi/metagenomicReport
oicr-gsi/mixcr
MiXCr identifies reads for V, D, J segment genes and quantifies antibody diversity
oicr-gsi/mutect
Workflow for Mutect1 somatic variant calling
oicr-gsi/mutect2ConsensusTumorOnly
The Mutect2Consensus workflow with only tumor inputs
oicr-gsi/nanoplot
Workflow to run Nanoplot (Plotting tool for long read sequencing data and alignments)
oicr-gsi/novoBreak
WDL workflow for novoBreak (https://github.com/czc/nb_distribution)
oicr-gsi/starFusion
Workflow that takes a fastq pair or optionally a chimeric file from STAR and detects RNA-seq fusion events.
oicr-gsi/strelka
Workflow to run Strelka1 for variant calling
oicr-gsi/trust4
analysis of antibody diversity, .wdl wrapper workflow
oicr-gsi/umiQC
QC workflow to assess UMI components
oicr-gsi/varscan
varscan repo contains code for Varscan workflow
oicr-gsi/virusbreakend
OICR Genomics WDL for VIRUSBreakend
oicr-gsi/wgsMetrics
Wrapper for picard WGSMetrics
oicr-gsi/xenoclassify-workflow
workflow to classify short-read sequencing data generated from xenograft samples