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ampliconpipeline

:poultry_leg: Pipeline for processing OLC 16S MiSeq runs with QIIME 2

autointerop

:floppy_disk: A Python tool for automatically running Illumina InterOp software on MiSeq run output

autorogav2

:ledger: Code to automatically produce OLC reports of genomic analysis

cchsnutritionviz

Prototyping for CCHS nutrition visualization

databasev2

download_refseq

:arrow_down: Facilitates downloading NCBI's RefSeq with a human-readable file structure

fetagenome_generator

WIP

genesipprv2

genomeannouncements

genomeqaml_gui

:camel: GUI wrapper for the OLC GenomeQAML

metaanalyzer

Personal tool wrapper scripts for processing metagenomic datasets

mgrastpull

Script for pulling metagenomic data using MG-RAST-TOOLS

olc_nas_tools

Internal OLC program to retrieve sequence data from the local FreeNAS

olc_webportalv2

:cloud: A web portal to provide a simple interface for bioinformatics analysis with support for multiple CFIA users.

olcredmineautomator

:loop: Program to monitor the OLC Redmine instance for automated bioinformatics job requests

run_metaphlan2

Simple wrapper for quickly running MetaPhlAn2+GraPhlan+HUMAnN2

scrubmed

Retrieves all PubMed article abstracts/other metadata from a provided query

sipping_portal

:tropical_drink: Local Django application for running GenesipprV2 against active MiSeq runs

snapperdb_automator

Internal helper program to populate SnapperDB with data. WIP.

variantpipe

Pipeline for variant calling with NGS data