Pinned Repositories
api.gtdb.ecogenomic.org
https://api.gtdb.ecogenomic.org/
BamM
Metagenomics-focused BAM file manipulation
basespace_project_downloader
Download project fastq files from BaseSpace
CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
FrankenQIIME
Feel the Franken
gtdb-itol-decorate
Creates iTOL files for tree decoration, given a set of GTDB genomes.
gtdb-species-clusters
Toolkit for establishing, updating, and validating GTDB species clusters
GTDBNCBI
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.
GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Mannotator
Microbial annotation pipeline - in progress
Australian Centre for Ecogenomics's Repositories
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Ecogenomics/CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Ecogenomics/gtdb-species-clusters
Toolkit for establishing, updating, and validating GTDB species clusters
Ecogenomics/BamM
Metagenomics-focused BAM file manipulation
Ecogenomics/GTDBNCBI
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.
Ecogenomics/gtdb-itol-decorate
Creates iTOL files for tree decoration, given a set of GTDB genomes.
Ecogenomics/api.gtdb.ecogenomic.org
https://api.gtdb.ecogenomic.org/
Ecogenomics/basespace_project_downloader
Download project fastq files from BaseSpace
Ecogenomics/ace-guix
GNU Guix package definitions for ACE or otherwise
Ecogenomics/gtdb.ecogenomic.org
https://gtdb.ecogenomic.org/
Ecogenomics/mingle
Australian Centre for Ecogenomics' genome tree database: Taxonomically annotated trees from HMMs and BLAST
Ecogenomics/ScaffoldM
scaffoldm
Ecogenomics/ace-cluster-orchestrator
A template for distributing jobs across the ACE cluster.
Ecogenomics/gtdb-migration-tk
Toolkit for updating the GTDB to the next release and test data
Ecogenomics/gtdb-release-tk
Toolkit for updating the GTDB to the next release and generating data files for the GTDB website.
Ecogenomics/hatchet
Tools used to split the GTDB-Tk reference tree into smaller sub trees
Ecogenomics/pfam_search
pfam_scan meets hmmsearch.
Ecogenomics/PhylogeneticM
Feed the tree...
Ecogenomics/slamM
slamM: a hybrid metagenomic assembly pipeline
Ecogenomics/ace-conda
ACE specific conda configuration packages.
Ecogenomics/ace_seq_job_downloader
Script for downloading data from ACE Sequencing
Ecogenomics/APP
Ace Pyrotag Pipeline - wrapper for QIIME and R - interfaces with PyroDB
Ecogenomics/data.gtdb.ecogenomic.org
https://data.gtdb.ecogenomic.org/
Ecogenomics/db.gtdb.ecogenomic.org
GTDB database service
Ecogenomics/DeltaPD
DeltaPD is a tool used to determine outliers in a gene tree when compared against a reference tree.
Ecogenomics/gtdb-lib
An abstraction of objects, files, and third-party tools used by the GTDB. Not intended for public use.
Ecogenomics/gtdb_precurate
Automatic pre-curation of GTDB trees.
Ecogenomics/gtdblib
Ecogenomics/GTDBLite
Ecogenomics/scripts
Public scripts referenced in ACE manuscripts