wwood
Assoc. prof. of microbial informatics at the Centre for Microbiome Research (CMR)
Queensland University of TechnologyBrisbane, Australia
Pinned Repositories
aviary
A hybrid assembly and MAG recovery pipeline (and more!)
Lorikeet
Strain resolver for metagenomics
bbbin
A collection of working and non-working bioinformatics scripts
CoverM
Read coverage calculator for metagenomics
galah
More scalable dereplication for metagenome assembled genomes
goruby
Gene Ontology (GO) interface for Ruby
kingfisher-download
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
OrfM
simple and not slow ORF caller
rarff
(fork) A Ruby library for handling ARFF files, as popularized by the WEKA machine learning program
singlem
Novelty-inclusive microbial community profiling of shotgun metagenomes
wwood's Repositories
wwood/CoverM
Read coverage calculator for metagenomics
wwood/kingfisher-download
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
wwood/singlem
Novelty-inclusive microbial community profiling of shotgun metagenomes
wwood/galah
More scalable dereplication for metagenome assembled genomes
wwood/bbbin
A collection of working and non-working bioinformatics scripts
wwood/hmmer-rs
Ergonomic Rust interface to HMMER
wwood/bacterial_dating_aerobic_predictor
Prediction of aerobicity in extant and ancient genomes
wwood/smafa
Biological sequence aligner for pre-aligned sequences
wwood/mfqe
FASTA/FASTQ extractor for multiple sets of read names
wwood/bird_tool_utils-rust
Utility functions for the bird metagenomic toolkit
wwood/sandpiper
Website / continuous DB builds for SingleM
wwood/bird_tool_utils-python
Opinionated Python utilities used in the bird suite of bioinformatic tools, developed by the Woodcroft lab
wwood/checkm-rs
Rust library for CheckM genome assessor
wwood/prodigal-runner
Run prodigal on microbial genomes automatically choosing between translation tables 4 and 11.
wwood/SilkSlider
Predict silk-like proteins
wwood/singlem-benchmarking
wwood/singlem-installation
Containerised testing of SingleM installation methods
wwood/singlem_host_or_ecological_predictor
Predict whether a metagenome is from a host-associated sample or not based on its SingleM profile
wwood/templates
A set of GPL templates which make coding more funner!
wwood/Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
wwood/tree2tax
Automatic taxonomy through consistent application of tree-based thresholding
wwood/bioconda-recipes
Conda recipes for the bioconda channel.
wwood/gtdb2ncbi
GTDB => NCBI
wwood/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
wwood/P6-BinChilling
P6
wwood/public_sequencing_metadata_corrections
Corrections to publicly available (e.g. at NCBI) metadata associated with sequencing data
wwood/singlem-sra-processing
Internal pipelines for singlem+sandpiper
wwood/skani
Fast, robust ANI and aligned fraction for metagenomic genomes and contigs.
wwood/sracat
Quickly extract sequence (and quality scores) from Sequence Read Archive records
wwood/zenodo_backpack-feedstock
A conda-smithy repository for zenodo_backpack.