Nick Youngblut's repositories
gtdb_to_taxdump
Convert GTDB taxonomy to NCBI taxdump format
StrainFacts
Factorize metagenotypes to infer strains and their abundances
alphafold
Open source code for AlphaFold.
alphafold_sm
snakemake wrapper for alphafold
ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
anvio
An analysis and visualization platform for 'omics data
bioconda-recipes
Conda recipes for the bioconda channel.
DataSci-BoilerPlate
Boiler plate code for data science projects
dotfiles
dotfile store
endoR
R-package to simplify tree ensemble models to decision ensemble, calculate feature and interaction importance, and construct variable networks.
kraken2
The second version of the Kraken taxonomic sequence classification system
nanoseq
Nanopore demultiplexing, QC and alignment pipeline
nextflow
A DSL for data-driven computational pipelines
nf-tower-aws
Repository containing required policies for Nextflow Tower deployment on AWS
phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
ResMiCo
Identifying misassemblies via deep learning
rocker
R configurations for Docker
sangeranalyseR
functions to analyse sanger sequencing reads in R
ScreenPro2
Genome-scale or custom CRISPR screen analysis for single gene or combinatorial libraries.
shinyTime
A timeInput widget for Shiny
SPeDE
A python application for MALDI-TOF MS dereplication
StrainGE
strain-level analysis tools
StrainScan
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
tmhmm.py
A transmembrane helix finder in Python 3.
veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes