Pinned Repositories
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
docker-containers
Docker containers for bioinformatic tools
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
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!
gregorysprenger's Repositories
gregorysprenger/bacterial-genomics-assembly-workflow
pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data
gregorysprenger/bio-agents_and_precip
Using public data to look at correlations between agents and precipitation.
gregorysprenger/BLAST2Sequences
Recreation of the web-based BLAST tool
gregorysprenger/configs
Config files used to define parameters specific to compute environments at different Institutions
gregorysprenger/docker-containers
Docker containers for bioinformatic tools
gregorysprenger/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
gregorysprenger/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!
gregorysprenger/docker-dragen
Dragen for Docker
gregorysprenger/krakenSankey
a re-packaging of the sankey plot function for kraken reports taken from pavian and sankeyD3 from Florian Breitwieser
gregorysprenger/mag
Assembly and binning of metagenomes
gregorysprenger/metagenomics-reproducibility
Reproducing results from a published metagenomic paper.
gregorysprenger/miga
MiGA: Microbial Genomes Atlas
gregorysprenger/Netflix-to-Trakt-Import
Synchronize/Import the viewing history from Netflix to trakt.tv
gregorysprenger/nf-co.re
Code and files for the main nf-core website.
gregorysprenger/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.
gregorysprenger/test-datasets
Test data to be used for automated testing with the nf-core pipelines
gregorysprenger/tools
Python package with helper tools for the nf-core community.
gregorysprenger/wf-aai
Perform average amino acid identity (AAI) on 2 or more proteomes.
gregorysprenger/wf-ani
Perform Average Nucleotide Identity (ANI) on FastA/Genbank files.
gregorysprenger/wf-assembly-snps
gregorysprenger/wf-cgmlst-gustle
gregorysprenger/wf-paired-illumina-read-clean
gregorysprenger/wf-pocp
WARN: This pipeline has been merged with wf-aai. Compute Percentage of Conserved Proteins (POCP) between FastA and GenBank files
gregorysprenger/wf-template
Example template of a Nextflow workflow
gregorysprenger/wf-vsnp