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3841_contig_snp_identification

Contig mapping and SNP identification against Rlv3841 NCBI genome

aroneys.github.io

A beautiful, simple, clean, and responsive Jekyll theme for academics

aviary

A hybrid assembly and MAG recovery pipeline (and more!)

binchicken

Bin chicken - targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly

bioconda-recipes

Conda recipes for the bioconda channel.

bird_tool_utils-python

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

capillary-tracking

cazyme_scraper

A custom R-script to scrape the list of experimentally characterized cazymes from the cazymes website.

checkm-rs

Rust library for CheckM genome assessor

conda_env_yamls

Conda environment definition yaml files for various programs

coverm

Read coverage calculator for metagenomics

cross_db_analysis

Compare singleM databases formed from reads, assemblies and bins

cv

dram

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

dram_annotation_extract_pathway

emerge_pipline

The pipline for the folks at emerge, they will want it eventualy

fluorescent_drop_counter

galah

More scalable dereplication for metagenome assembled genomes

get_matches_no_dup

graftm

GraftM - Rapid community profiles from metagenomes

gtdbtk

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

hpc_scripts

Scripts for easier use of the QUT HPC system

metabolome_permafrost

This repository includes code for the analyses and figures presented in the manuscript

misc_scripts

my_first_rails_app

nodule-segmentation

oxdown

An updated R Markdown thesis template using the bookdown package

prn_data_extract

Extract from our raw exports to flat files with geo coded lat / lons from subject metadata

rest_python

Python REST tutorial

simple_sinatra_minitest