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2019-04-08-nextflow-presentation-reveal-cljs

Intro presentation on Nextflow given 2019-04-08

2020-08-20-nextflow-presentation-reveal-cljs

An Intro to Nextflow (2020-08-20)

analysis-of-human-iav-ha-genes

aodp

Automated Oligonucleotide Design Pipeline (AODP) from https://bitbucket.org/wenchen_aafc/aodp_v2.0_release/

bertax

Taxonomic classification of DNA sequences

bioconda-recipes

Conda recipes for the bioconda channel.

biohansel

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

blast2xl

BLAST XLSX Report Creator and Sequence Sorter

cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

docker-iqtree

IQ-TREE Alpine Docker container

docker-minknow

Install and run Oxford Nanopore's MinKNOW software on other Linux distros

docker-tvc-tmap-torrent-suite

Docker container for compiled TMAP and TVC tools from the Thermo Fisher Ion Torrent Suite

enteritidis_subtyping

fast5watch

Nanopore run watcher

fasta2lmdb

Quickly save FASTA sequences to an LMDB key-value database for rapid retrieval.

filter_classified_reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

galaxy_tools

Contains a set of Galaxy Tools mostly written by the Bioinformatics core at NML

genotyphi

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

ggstatsplot

Enhancing `ggplot2` plots with statistical analysis 📊🎨📣

guppywuppy

Basic service wrapping PyGuppyClient talking to fast5watch

heidelberg_subtyping

Subtype Salmonella enterica subsp. enterica serovar Heidelberg genomes using an in-silico 33 bp k-mer subtyping method developed by Genevieve Labbe, Roger Johnson, et al from the Public Health Agency of Canada.

hello-github-actions

irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

irida-uploader

Sequence file uploader for IRIDA

irma

Iterative Refinement Meta-Assembler

irma-singularity

ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

jquery-file-upload

File Upload widget with multiple file selection, drag&drop support, progress bars and preview images for jQuery. Supports cross-domain, chunked and resumable file uploads and client-side image resizing. Works with any server-side platform (PHP, Python, Ruby on Rails, Java, Node.js, Go etc.) that supports standard HTML form file uploads.