ecogenomics Goto Github PK

ace-cluster-orchestrator

A template for distributing jobs across the ACE cluster.

ace-conda

ACE specific conda configuration packages.

ace-guix

GNU Guix package definitions for ACE or otherwise

ace_seq_job_downloader

Script for downloading data from ACE Sequencing

api.gtdb.ecogenomic.org

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

app

Ace Pyrotag Pipeline - wrapper for QIIME and R - interfaces with PyroDB

bamm

Metagenomics-focused BAM file manipulation

basespace_project_downloader

Download project fastq files from BaseSpace

bioscripts

A collection of scripts written by ACE members

checkm

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

data.gtdb.ecogenomic.org

https://data.gtdb.ecogenomic.org/

db.gtdb.ecogenomic.org

GTDB database service

deltapd

DeltaPD is a tool used to determine outliers in a gene tree when compared against a reference tree.

frankenqiime

Feel the Franken

gtdb-itol-decorate

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

gtdb-lib

An abstraction of objects, files, and third-party tools used by the GTDB. Not intended for public use.

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.

gtdb-species-clusters

Toolkit for establishing, updating, and validating GTDB species clusters

gtdb.ecogenomic.org

https://gtdb.ecogenomic.org/

gtdb_precurate

Automatic pre-curation of GTDB trees.

gtdblib

gtdblite

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.

hatchet

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

ionpairer

create a rough scaffold using ion torrent MP reads

mannotator

Microbial annotation pipeline - in progress

mingle

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

mungegg

Join a taxonomy to the greengenes database