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miso-lims-docker

Docker container for miso-lims

mixcr

MiXCr identifies reads for V, D, J segment genes and quantifies antibody diversity

mmrdetect

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

modeltsne

A t-SNE framework to visualize OMICs data

mrdetect

workflow to detect Minimal Residual disease with MRDetect

msisensor

msisensor-pro workflow

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

mutagene

a WDL implementation of mutagene signature detection

mutect

Workflow for Mutect1 somatic variant calling

mutect2

Workflow to run Mutect2 (GATK4)

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.

mutect2consensustumoronly

The Mutect2Consensus workflow with only tumor inputs

nabu

QC tracking for files via a web service

nanoplot

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

nanopore-sv-analysis

Structural variant filtering and anlaysis of Nanopore human WGS data.

nanoporecoverageanalysis

Workflow for nanopore coverage analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporefilterfastq

Workflow for filter nanopore fastq file, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporemapping

Workflow for nanopore reads mapping, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporerunsvanalysis

Workflow for running structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

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.

ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

ncov2019articnf

ncov2019ArticNf workflow executes the ncov2019-artic-nf Nextflow workflow from connor-lab (https://github.com/connor-lab/ncov2019-artic-nf).

ncov2019articnfnanopore

This Nextflow pipeline automates the ARTIC network nCoV-2019 novel coronavirus bioinformatics protocol.

neatdatastructures

This is the repository for code which uses human genomic data to create data structures for the NEAT genomic read simulator.

neoantigen-mutation-burden

nextflow_wg_pipeline

node-starter-kit

Basic setup for a new Node project

novobreak

WDL workflow for novoBreak (https://github.com/czc/nb_distribution)

oicr-gsi.github.io

Website for Genome Sequence Informatics

panelcnmops

Workflow to run panelcn.MOPS for CNVs in targeted sequencing