Gregory Sprenger's repositories
configs
Config files used to define parameters specific to compute environments at different Institutions
docker-containers
Docker containers for bioinformatic tools
bacterial-genomics-assembly-workflow
pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data
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-pocp
WARN: This pipeline has been merged with wf-aai. Compute Percentage of Conserved Proteins (POCP) between FastA and GenBank files
Netflix-to-Trakt-Import
Synchronize/Import the viewing history from Netflix to trakt.tv
tools
Python package with helper tools for the nf-core community.
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!
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
mag
Assembly and binning of metagenomes
krakenSankey
a re-packaging of the sankey plot function for kraken reports taken from pavian and sankeyD3 from Florian Breitwieser
nf-co.re
Code and files for the main nf-core website.
miga
MiGA: Microbial Genomes Atlas
bio-agents_and_precip
Using public data to look at correlations between agents and precipitation.
wf-template
Example template of a Nextflow workflow
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
metagenomics-reproducibility
Reproducing results from a published metagenomic paper.
BLAST2Sequences
Recreation of the web-based BLAST tool