ecogenomics Goto Github PK
Name: Australian Centre for Ecogenomics
Type: Organization
Location: University of Queensland, Australia
Blog: ecogenomic.org
Name: Australian Centre for Ecogenomics
Type: Organization
Location: University of Queensland, Australia
Blog: ecogenomic.org
A template for distributing jobs across the ACE cluster.
ACE specific conda configuration packages.
GNU Guix package definitions for ACE or otherwise
Script for downloading data from ACE Sequencing
https://api.gtdb.ecogenomic.org/
Ace Pyrotag Pipeline - wrapper for QIIME and R - interfaces with PyroDB
Metagenomics-focused BAM file manipulation
Download project fastq files from BaseSpace
A collection of scripts written by ACE members
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://data.gtdb.ecogenomic.org/
GTDB database service
DeltaPD is a tool used to determine outliers in a gene tree when compared against a reference tree.
Feel the Franken
Creates iTOL files for tree decoration, given a set of GTDB genomes.
An abstraction of objects, files, and third-party tools used by the GTDB. Not intended for public use.
Toolkit for updating the GTDB to the next release and test data
Toolkit for updating the GTDB to the next release and generating data files for the GTDB website.
Toolkit for establishing, updating, and validating GTDB species clusters
https://gtdb.ecogenomic.org/
Automatic pre-curation of GTDB trees.
The GTDB provides the software infrastructure for working with a large collection of genomic resources. The major goal of this initiative is to provide a phylogenetically consistent taxonomy for archaea and bacteria.
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Tools used to split the GTDB-Tk reference tree into smaller sub trees
create a rough scaffold using ion torrent MP reads
Microbial annotation pipeline - in progress
Australian Centre for Ecogenomics' genome tree database: Taxonomically annotated trees from HMMs and BLAST
Join a taxonomy to the greengenes database
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