wwood
Assoc. prof. of microbial informatics at the Centre for Microbiome Research (CMR)
Queensland University of TechnologyBrisbane, Australia
Pinned Repositories
binchicken
Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly
aviary
A hybrid assembly and MAG recovery pipeline (and more!)
Lorikeet
Strain resolver for metagenomics
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/dirseq
Work out whether RNAseq reads in general agree with the direction of the gene predicted
wwood/enrichM
wwood/bird_tool_utils-python
Opinionated Python utilities used in the bird suite of bioinformatic tools, developed by the Woodcroft lab
wwood/extern
Convenient python shell command running library
wwood/guix
wwood/Lorikeet
Strain resolver for metagenomics
wwood/tree2tax
Automatic taxonomy through consistent application of tree-based thresholding
wwood/abisko-stuff
Abisko project-specific R scripts (and maybe more later)
wwood/ALE
Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
wwood/argparse-manpage-birdtools
Automatically build man-pages for your Python project
wwood/aviary
A snakemake pipeline for binning metagenomic assemblies
wwood/aws-genomics-workflows
Genomics Workflows on AWS
wwood/biolib
Python package for common tasks in bioinformatic.
wwood/bird_tool_utils-man
Generate structured man pages
wwood/DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
wwood/GeneTreeTk
A toolbox for working with gene trees.
wwood/graftM
GraftM - Rapid community profiles from metagenomes
wwood/gtdb2ncbi
GTDB => NCBI
wwood/guix_mine
A collection of guix package definitions not in the main repository (some may transit there in time)
wwood/kingfisher-benchmarking
Benchmarking for the kingfisher tool
wwood/KWAGE
Ultra-fast, Bloom filter-based sequence search
wwood/luca_scripts
scripts for working on a supercomputer
wwood/phanotate-scripts
Various scripts for calling circular genes with PHANOTATE
wwood/RecurM
Detecting repeatedly assembled genomic units in metagenome data
wwood/rosella
Metagenomic Binning Algorithm
wwood/rust-debruijn
De Bruijn graphs in Rust
wwood/rust-pseudoaligner
Single-Cell RNA-seq pseudo-aligner
wwood/singlem-wdl
Code for running SingleM through AWS Batch + Cromwell.
wwood/sracat
Quickly extract sequence (and quality scores) from Sequence Read Archive records
wwood/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks