Genome Sequence Informatics

shesmu

Decision-driven action launching system

djerba

Create cancer bioinformatics reports from metadata and workflow output

variantEffectPredictor

Variant Effect Predictor Workflow

bwaMem

Workflow for BWA mem

delly

Delly workflow produces a set of vcf files with different types of structural variant calls

dimsum

QC Tracking dashboard

gsi-wdl-tools

pinery

A LIMS abstraction layer to provide generalized LIMS access via a web service.

vidarr

Analysis provenance tracking server

analysisProcedures

bwamem2

workflow for bwa-men2

cardea

Case data API

cerberus

File provenance library

dellyGermline

Call germline SVs using Delly

dnaSeqQC

DNASeqQC Pipeline; chains bwaMem, fastQC, and bamQC

Dragen-Align

Lane Level (single fastq pair) alignments using Dragen

dragmap

A workflow to run Dragmap

empty

Empty workflow for testing infrastructure

hisat2

Workflow for hisat2, a graph-based aligner

hotspotFingerprintCollector

common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools

mavis3

MAVIS workflow, annotation of structural variants

minimap2

Workflow to align long read fastq files to a reference genome

mrdetect

workflow to detect Minimal Residual disease with MRDetect

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.

nabu

QC tracking for files via a web service

provenanceReporter

t1k

umiCollapse

umiCollapse workflow, generating umi deduplicated bam file and stats

vidarr-tools

The home of Python tools for use with Víðarr

xenoclassify-workflow

workflow to classify short-read sequencing data generated from xenograft samples