kraken-biom VS taxopedia

Compare kraken-biom vs taxopedia 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)
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kraken-biom taxopedia
1 4
50 7
- -
0.0 0.0
almost 3 years ago about 3 years ago
Python Python
MIT License MIT License
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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).

taxopedia

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

What are some alternatives?

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

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

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).

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

Wikipedia-API - Python wrapper for Wikipedia

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

Wikipedia-Article-Scraper - A complete Python text analytics package that allows users to search for a Wikipedia article, scrape it, conduct basic text analytics and integrate it to a data pipeline without writing excessive code.

drep - Rapid comparison and dereplication of genomes

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

wikiteam - Tools for downloading and preserving wikis. We archive wikis, from Wikipedia to tiniest wikis. As of 2024, WikiTeam has preserved more than 600,000 wikis.

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