Pinned Repositories
crowbar
csv2xlsx
Wraps CSV files in a MS Excel workbook, with each CSV as a worksheet.
fsac
fairly simple allele caller
grapetree_cluster
Cluster GrapeTree's output into clusters
host-snap
Removes specific viral sequences from a host genome and generates a SNAP index
pangenome
Wraps Panseq to quickly create pangenomes for in silico typing
pangenome_extract
snakefiles
Snakefiles for reproducible analyses
snakemake-intro
An introduction to Snakemake, taught as three one-hour classes
voc-identify
Identify Variants of Concern from metagenomic samples of SARS-CoV-2
dorbarker's Repositories
dorbarker/voc-identify
Identify Variants of Concern from metagenomic samples of SARS-CoV-2
dorbarker/snakemake-intro
An introduction to Snakemake, taught as three one-hour classes
dorbarker/crowbar
dorbarker/fsac
fairly simple allele caller
dorbarker/rackham
cgMLST defintion from PIRATE pangenomes
dorbarker/snakefiles
Snakefiles for reproducible analyses
dorbarker/CGFPrediction
dorbarker/cohortid
dorbarker/comersatz
Construct synthetic metagenomes from sequencing read data
dorbarker/cookbook
A Cookbook of Short Solutions to Various Bioinformatics Problems
dorbarker/disseqt-redux
Refactoring DISSEQT
dorbarker/endless-sky
Space exploration, trading, and combat game.
dorbarker/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.
dorbarker/extract_aligned_region
Extract the regions of a reference genome mapped by sequencing reads
dorbarker/gogetem
Get nucleotide data from EMBL and amino acid data from UniProt for Gene Ontology terms
dorbarker/gtclust
dorbarker/kmer-mlst
Calling MLST alleles from reads using Aho-Corasick string matching
dorbarker/KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
dorbarker/maldease
MALDI data analysis on the command line
dorbarker/monomap
Find reads that mapped to reference A, but not to reference B.
dorbarker/nAWC
Neighbour Adjusted Wallace Coefficient for identifying cluster stability
dorbarker/PIRATE
A toolbox for pangenome analysis and threshold evaluation.
dorbarker/poster
dorbarker/pyrankvote
PyRankVote is a python library for different ranked-choice voting systems, like IRV, STV and PBV. Created in June 2019.
dorbarker/salmonella-heidelberg-cgmlst
A cgMLST scheme for Salmonella Heidelberg created using chewBBACA
dorbarker/table-intersect
Takes delimited files and writes a copy of each containing the intersect of the leftmost column of all the files.
dorbarker/tidy-gcpay
Convert the untidy XLSX output from MyGCPay into a nice and tidy TSV
dorbarker/VCFParser
Parse iVar output into beautiful heatmaps based on pre-defined list of SNVs associated with COVID-19 VOC/VOIs
dorbarker/Wallace.jl
Adjusted Wallace Coefficient implemented in Julia
dorbarker/wobbulator