wwood

CoverM

Read coverage calculator for metagenomics

kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes

galah

More scalable dereplication for metagenome assembled genomes

bbbin

A collection of working and non-working bioinformatics scripts

hmmer-rs

Ergonomic Rust interface to HMMER

bacterial_dating_aerobic_predictor

Prediction of aerobicity in extant and ancient genomes

smafa

Biological sequence aligner for pre-aligned sequences

mfqe

FASTA/FASTQ extractor for multiple sets of read names

bird_tool_utils-rust

Utility functions for the bird metagenomic toolkit

sandpiper

Website / continuous DB builds for SingleM

bird_tool_utils-python

Opinionated Python utilities used in the bird suite of bioinformatic tools, developed by the Woodcroft lab

checkm-rs

Rust library for CheckM genome assessor

prodigal-runner

Run prodigal on microbial genomes automatically choosing between translation tables 4 and 11.

SilkSlider

Predict silk-like proteins

singlem-benchmarking

singlem-installation

Containerised testing of SingleM installation methods

singlem_host_or_ecological_predictor

Predict whether a metagenome is from a host-associated sample or not based on its SingleM profile

templates

A set of GPL templates which make coding more funner!

Tome

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

tree2tax

Automatic taxonomy through consistent application of tree-based thresholding

bioconda-recipes

Conda recipes for the bioconda channel.

gtdb2ncbi

GTDB => NCBI

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

P6-BinChilling

P6

public_sequencing_metadata_corrections

Corrections to publicly available (e.g. at NCBI) metadata associated with sequencing data

singlem-sra-processing

Internal pipelines for singlem+sandpiper

skani

Fast, robust ANI and aligned fraction for metagenomic genomes and contigs.

sracat

Quickly extract sequence (and quality scores) from Sequence Read Archive records

zenodo_backpack-feedstock

A conda-smithy repository for zenodo_backpack.