kraken-biom VS GTDBTk

Compare kraken-biom vs GTDBTk and see what are their differences.

kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken). (by smdabdoub)
metagenomics taxonomy taxonomic-classification Bioinformatics kraken biom-format
Source Code
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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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kraken-biom GTDBTk
1 1
50 495
- 3.0%
0.0 6.7
almost 3 years ago about 2 months ago
Python Python
MIT License GNU General Public License v3.0 only
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kraken-biom

Posts with mentions or reviews of kraken-biom. We have used some of these posts to build our list of alternatives and similar projects.
  • Differences between read based abundancy estimation programs? (metagenomics)
    1 project | /r/bioinformatics | 7 Feb 2022
    The issue is that after performing a taxonomic classification using kraken2, I want to create abundance tables regarding this taxonomic classification outputs. Some people have recommended me to use kraken--biom (https://github.com/smdabdoub/kraken-biom) and some others recommended me to use bracken (https://ccb.jhu.edu/software/bracken/index.shtml?t=manual).

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.

What are some alternatives?

When comparing kraken-biom and GTDBTk you can also consider the following projects:

atlas - ATLAS - Three commands to start analyzing your metagenome data

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

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

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

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

drep - Rapid comparison and dereplication of genomes

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

taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.

GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

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

kraken-biom vs atlas GTDBTk vs dada2 kraken-biom vs dada2 GTDBTk vs bakta kraken-biom vs MMseqs2 GTDBTk vs CAT_pack kraken-biom vs drep GTDBTk vs phantasm kraken-biom vs taxopedia GTDBTk vs MMseqs2 kraken-biom vs GraphBin2 GTDBTk vs classify-genomes
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