GTDBTk VS pyani

Compare GTDBTk vs pyani and see what are their differences.

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. (by Ecogenomics)
taxonomy species-assignments Phylogenetics archaea bacteria nomenclature Bioinformatics metagenomics
Source Code
ecogenomics.github.io
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pyani

Application and Python module for average nucleotide identity analyses of microbes. (by widdowquinn)
Bioinformatics average-nucleotide-identity taxonomy taxonomy-assignment Classification ani
Source Code
widdowquinn.github.io
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GTDBTk pyani
1 1
435 180
4.4% -
7.5 9.0
16 days ago about 1 month ago
Python Python
GNU General Public License v3.0 only MIT License
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GTDBTk

Posts with mentions or reviews of GTDBTk. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-08-11.

pyani

Posts with mentions or reviews of pyani. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-10-20.
  • MAFFT Alignment taking longer than expected
    2 projects | /r/bioinformatics | 20 Oct 2022
    But to help you along, one would chop up the genomes into smaller bits to robustly handle potential re-arrangements. A classic tool to do so, is the MUMMER algorithm, which for your purpose is nicely implemented here: https://github.com/widdowquinn/pyani

What are some alternatives?

When comparing GTDBTk and pyani you can also consider the following projects:

kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

phantasm - PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

CAT_pack - CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

misp-taxonomies - Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.

MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite

dada2 - Accurate sample inference from amplicon data with single nucleotide resolution

classify-genomes - Classify a genome sequence according to the mOTUs/specI taxonomy

bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

GTDBTk vs kraken-biom pyani vs phantasm GTDBTk vs CAT_pack pyani vs misp-taxonomies GTDBTk vs MMseqs2 GTDBTk vs dada2 GTDBTk vs classify-genomes GTDBTk vs bakta GTDBTk vs phantasm