Genome Sequence Informatics

malta

Interface and tracking for clinical report generation

estimate

ESTIMATE provides researchers with scores for tumor purity, the level of stromal cells present, and the infiltration level of immune cells in tumor tissues based on expression data

sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

cellrangerAtacCount

cellrangerCount

WDL Workflow to run cellranger count

cfMeDIPs-bakeoff-report-infra

Code repo for the OICR bake-off analysis

CHORD

A WDL implementation of UMCUGenetics CHORD

cramConverter

a workflow to run bamToCram or cramToBam

fastqc

Workflow for FastQC

fastqs_release_tracker

Release information for each run and project for fastqs sequenced at OICR

gatk-genotype-GVCFs

Genotype GVCFs WDL workflow for GATK4

guppy

Workflow to run guppy basecaller and barcoder for nanopore data

hlavbseq

workflow wraps HLA-VBSeq, a tool for estimating the most prevalent HLA types in a sample

indelValidate

workflow for indel validation, based on CGI-Tools/6-indelValidate.sh

injectFastq

Check and inject fastq files

InsertSizeMetrics

Workflow to run picard InsertSizeMetrics

manta

MantaSV workflow

minimap2

Workflow to align long read fastq files to a reference genome

MMRDetect

MMRDetect is a mutational signature-based classifier for identifying tumors with mismatch repair deficiency using whole-genome sequencing data.

mutagene

a WDL implementation of mutagene signature detection

mutect

Workflow for Mutect1 somatic variant calling

nanoplot

Workflow to run Nanoplot (Plotting tool for long read sequencing data and alignments)

panelcnMOPS

Workflow to run panelcn.MOPS for CNVs in targeted sequencing

qcthresholds

sarsCoV2ArticNf

SAUCR

Web interface to examine and compare sample fingerprints

sniffles

Workflow to run Structural Variant caller for Nanopore

svtools

Tools for processing and analyzing structural variants.

tape-archiving

Scripts meant to prepare a project for archiving, encrypt it using GPG, verify the output, and then send it to CommVault to write to tape

wdlviz

Python tool to create DOT diagrams for WDL workflows