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bacterial-genomics-assembly-workflow

pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data

bio-agents_and_precip

Using public data to look at correlations between agents and precipitation.

blast2sequences

Recreation of the web-based BLAST tool

configs

Config files used to define parameters specific to compute environments at different Institutions

docker-containers

Docker containers for bioinformatic tools

docker-dragen

Dragen for Docker

krakensankey

a re-packaging of the sankey plot function for kraken reports taken from pavian and sankeyD3 from Florian Breitwieser

lepto-in-silico-pcr

Using PCR primers from Barragan et al. (2016) to see if they are able to detect all pathogenic, intermediate, and saprophytic Leptospira. Source = High Leptospira Diversity in Animals and Humans Complicates the Search for Common Reservoirs of Human Disease in Rural Ecuador

mag

Assembly and binning of metagenomes

metagenomics-reproducibility

Reproducing results from a published metagenomic paper.

miga

MiGA: Microbial Genomes Atlas

netflix-to-trakt-import

Synchronize/Import the viewing history from Netflix to trakt.tv

nf-co.re

Code and files for the main nf-core website.

taxtriage

TaxTriage is designed in concordance with CDC recommendations to provide clinical environments the necessary tools to generate classification reports (using Kraken2) in a metagenomics scope. It is bundled with Nextflow to provide a seamless installation and usage experience.

test-datasets

Test data to be used for automated testing with the nf-core pipelines

tools

Python package with helper tools for the nf-core community.

wf-aai

Perform average amino acid identity (AAI) on 2 or more proteomes.

wf-ani

Perform Average Nucleotide Identity (ANI) on FastA/Genbank files.

wf-assembly-snps

wf-cgmlst-gustle

wf-paired-end-illumina-assembly

WARN: Repository has moved. Use the link below or link at the top of README to access the most up to date assembly pipeline!

wf-paired-illumina-read-clean

wf-pocp

WARN: This pipeline has been merged with wf-aai. Compute Percentage of Conserved Proteins (POCP) between FastA and GenBank files

wf-template

Example template of a Nextflow workflow

wf-vsnp