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
492 200
2.4% -
6.7 8.4
about 1 month ago 3 months 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.

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

fideslang - Open-source description language for privacy to declare data types and data behaviors in your tech stack in order to simplify data privacy globally. Supports GDPR, CCPA, LGPD and ISO 19944.

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

tutorials - In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given that you give proper credit. Have fun!

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

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

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