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@Ecogenomics Australian Centre for Ecogenomics

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    37 repositories

    • gtdb-species-clusters

      Public
      Toolkit for establishing, updating, and validating GTDB species clusters
      Python
      •
      Other
      •3•20•0•0•Updated Oct 11, 2024Oct 11, 2024

    • gtdb-migration-tk

      Public
      Toolkit for updating the GTDB to the next release and test data
      Python
      •0•1•0•0•Updated Oct 11, 2024Oct 11, 2024

    • GTDBTk

      Public
      GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
      bioinformaticsnomenclaturetaxonomymetagenomicsphylogeneticsbacteriaarchaeaspecies-assignments
      Python
      •
      GNU General Public License v3.0
      •82•473•22•0•Updated Sep 11, 2024Sep 11, 2024

    • gtdb.ecogenomic.org

      Public
      https://gtdb.ecogenomic.org/
      Vue
      •1•2•8•0•Updated Sep 3, 2024Sep 3, 2024

    • api.gtdb.ecogenomic.org

      Public
      https://api.gtdb.ecogenomic.org/
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Sep 3, 2024Sep 3, 2024

    • CheckM

      Public
      Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
      Python
      •
      GNU General Public License v3.0
      •73•341•14•1•Updated Sep 3, 2024Sep 3, 2024

    • gtdb-release-tk

      Public
      Toolkit for updating the GTDB to the next release and generating data files for the GTDB website.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Jul 3, 2024Jul 3, 2024

    • data.gtdb.ecogenomic.org

      Public
      https://data.gtdb.ecogenomic.org/
      XSLT
      •0•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • gtdb_precurate

      Public
      Automatic pre-curation of GTDB trees.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • GTDBNCBI

      Public
      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.
      Python
      •
      GNU General Public License v3.0
      •2•9•17•0•Updated Oct 30, 2023Oct 30, 2023

    • gtdb-lib

      Public
      An abstraction of objects, files, and third-party tools used by the GTDB. Not intended for public use.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 17, 2023Apr 17, 2023

    • gtdb-itol-decorate

      Public
      Creates iTOL files for tree decoration, given a set of GTDB genomes.
      Python
      •
      GNU General Public License v3.0
      •0•4•4•0•Updated Nov 3, 2022Nov 3, 2022

    • db.gtdb.ecogenomic.org

      Public
      GTDB database service
      Shell
      •0•0•0•0•Updated May 27, 2022May 27, 2022

    • hatchet

      Public
      Tools used to split the GTDB-Tk reference tree into smaller sub trees
      Python
      •0•1•0•0•Updated May 16, 2022May 16, 2022

    • ace-cluster-orchestrator

      Public
      A template for distributing jobs across the ACE cluster.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 8, 2022Mar 8, 2022

    • slamM

      Public
      slamM: a hybrid metagenomic assembly pipeline
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 10, 2021Mar 10, 2021

    • ace-conda

      Public
      ACE specific conda configuration packages.
      Shell
      •0•0•0•0•Updated Mar 2, 2021Mar 2, 2021

    • DeltaPD

      Public
      DeltaPD is a tool used to determine outliers in a gene tree when compared against a reference tree.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Dec 2, 2020Dec 2, 2020

    • scripts

      Public
      Public scripts referenced in ACE manuscripts
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 26, 2020Mar 26, 2020

    • ace-guix

      Public
      GNU Guix package definitions for ACE or otherwise
      Scheme
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Nov 23, 2019Nov 23, 2019

    • BamM

      Public
      Metagenomics-focused BAM file manipulation
      C
      •
      GNU Lesser General Public License v3.0
      •7•16•12•0•Updated Jul 8, 2019Jul 8, 2019

    • basespace_project_downloader

      Public
      Download project fastq files from BaseSpace
      Python
      •0•3•1•1•Updated Nov 13, 2017Nov 13, 2017

    • mingle

      Public
      Australian Centre for Ecogenomics' genome tree database: Taxonomically annotated trees from HMMs and BLAST
      Python
      •
      GNU General Public License v3.0
      •2•2•4•1•Updated May 13, 2017May 13, 2017

    • ace_seq_job_downloader

      Public
      Script for downloading data from ACE Sequencing
      Python
      •0•0•0•0•Updated Feb 2, 2017Feb 2, 2017

    • gtdblib

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 29, 2016Nov 29, 2016

    • GTDBLite

      Public archive
      Python
      •4•0•9•0•Updated Oct 29, 2015Oct 29, 2015

    • pfam_search

      Public
      pfam_scan meets hmmsearch.
      Perl
      •2•1•0•0•Updated Sep 17, 2015Sep 17, 2015

    • ScaffoldM

      Public
      scaffoldm
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 21, 2015May 21, 2015

    • APP

      Public archive
      Ace Pyrotag Pipeline - wrapper for QIIME and R - interfaces with PyroDB
      Perl
      •3•0•11•0•Updated Apr 4, 2014Apr 4, 2014

    • PhylogeneticM

      Public archive
      Feed the tree...
      Python
      •1•1•1•0•Updated Mar 11, 2013Mar 11, 2013