Dillon Barker's repositories
extract_aligned_region
Extract the regions of a reference genome mapped by sequencing reads
comersatz
Construct synthetic metagenomes from sequencing read data
ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
endless-sky
Space exploration, trading, and combat game.
maldease
MALDI data analysis on the command line
KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
gogetem
Get nucleotide data from EMBL and amino acid data from UniProt for Gene Ontology terms
snakemake-intro
An introduction to Snakemake, taught as three one-hour classes
PIRATE
A toolbox for pangenome analysis and threshold evaluation.
voc-identify
Identify Variants of Concern from metagenomic samples of SARS-CoV-2
VCFParser
Parse iVar output into beautiful heatmaps based on pre-defined list of SNVs associated with COVID-19 VOC/VOIs
kmer-mlst
Calling MLST alleles from reads using Aho-Corasick string matching
Wallace.jl
Adjusted Wallace Coefficient implemented in Julia
pyrankvote
PyRankVote is a python library for different ranked-choice voting systems, like IRV, STV and PBV. Created in June 2019.
nAWC
Neighbour Adjusted Wallace Coefficient for identifying cluster stability
table-intersect
Takes delimited files and writes a copy of each containing the intersect of the leftmost column of all the files.
cookbook
A Cookbook of Short Solutions to Various Bioinformatics Problems
snakefiles
Snakefiles for reproducible analyses
disseqt-redux
Refactoring DISSEQT
tidy-gcpay
Convert the untidy XLSX output from MyGCPay into a nice and tidy TSV
salmonella-heidelberg-cgmlst
A cgMLST scheme for Salmonella Heidelberg created using chewBBACA