Ecogenomics/PhylogeneticM

This repository has been archived on 30/Sep/2022
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Python
Created about 12 years ago
Updated over 11 years ago

Ecogenomics/PhylogeneticM

Ecogenomics

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GTDBTk

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

CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

gtdb-species-clusters

Toolkit for establishing, updating, and validating GTDB species clusters

BamM

Metagenomics-focused BAM file manipulation

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.

gtdb-itol-decorate

Creates iTOL files for tree decoration, given a set of GTDB genomes.

Mannotator

Microbial annotation pipeline - in progress

FrankenQIIME

Feel the Franken

basespace_project_downloader

Download project fastq files from BaseSpace

gtdb.ecogenomic.org

https://gtdb.ecogenomic.org/

ScaffoldM

ace-guix

GNU Guix package definitions for ACE or otherwise

mingle

Australian Centre for Ecogenomics' genome tree database: Taxonomically annotated trees from HMMs and BLAST

api.gtdb.ecogenomic.org

https://api.gtdb.ecogenomic.org/

ace-cluster-orchestrator

A template for distributing jobs across the ACE cluster.

gtdb-migration-tk

Toolkit for updating the GTDB to the next release and test data

gtdb-release-tk

Toolkit for updating the GTDB to the next release and generating data files for the GTDB website.

slamM

slamM: a hybrid metagenomic assembly pipeline

pfam_search

pfam_scan meets hmmsearch.

bioscripts

A collection of scripts written by ACE members

hatchet

Tools used to split the GTDB-Tk reference tree into smaller sub trees