taxopedia VS kraken-biom

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

taxopedia

Taxonomic trees (cladograms) from Wikipedia-scraped data. (by shanedrabing)
taxonomic-trees taxonomy Wikipedia wikipedia-scraper cladogram Phylogenetics phylogenetic-trees
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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
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taxopedia kraken-biom
4 1
7 43
- -
0.0 0.0
over 2 years ago about 2 years ago
Python Python
MIT License MIT License
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taxopedia

Posts with mentions or reviews of taxopedia. We have used some of these posts to build our list of alternatives and similar projects.

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).

What are some alternatives?

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

graphlan - High-quality circular representations of taxonomic and phylogenetic trees

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

ielex-data-and-tree - Data and scripts for producing a Baysian phylogenetic tree sample of for the Indo-European family which is "good enough", using data from IELex (Dunn et al. 2011).

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

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

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

drep - Rapid comparison and dereplication of genomes

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

taxopedia vs graphlan kraken-biom vs GTDBTk taxopedia vs ielex-data-and-tree kraken-biom vs MMseqs2 kraken-biom vs atlas kraken-biom vs dada2 kraken-biom vs drep kraken-biom vs GraphBin2