Matthew Wells's repositories
ecoli_serotyping
In silico prediction of E. coli serotype
SNVPhyl_Nextflow
Nextflow version of SNVPhyl
alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
AlleleCodes
Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies
biopython
Official git repository for Biopython (originally converted from CVS)
wordle-py
wordle on the terminal, I just want to play with creating solvers for it.
bug_report
Minimal reproducible example of bug involving nested schemas
chewBBACA
BSR-Based Allele Calling Algorithm
codon
A high-performance, zero-overhead, extensible Python compiler using LLVM
datasets
Benchmark and toy datasets
GTDBSketching
Convert a GTDB download into a Mash Sketch
hatch
Modern, extensible Python project management
HMAS-QC-Pipeline2
an alternative pipeline without using mothur
leviosam2
Fast and accurate coordinate conversion between assemblies
LexicHash
A novel method for sequence similarity estimation
line-by-line
Evaluating line-reading performance
lobster
The Lobster Programming Language
mikrokondo_tests
Test data sets for mikrokondo
MLSTDists
alternative to cgmlst-dists for mlst distance calculatoin
nf-flu
Influenza genome analysis Nextflow workflow
nf-validation
Params validation plugin for Nextflow pipelines
PilonPolisher
Iterative polishing with Pilon
racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
rasusa
Randomly subsample sequencing reads to a specified coverage
rustlings
:crab: Small exercises to get you used to reading and writing Rust code!
Sabres
A tool that scans VCF data for SARS-CoV-2 Antiviral Resistance
wtfpython
What the f*ck Python? 😱