kraken-biom VS dada2

Compare kraken-biom vs dada2 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
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dada2

Accurate sample inference from amplicon data with single nucleotide resolution (by benjjneb)
microbiome Bioinformatics bioconductor taxonomy amplicon metagenomics metabarcoding
Source Code
benjjneb.github.io
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kraken-biom dada2
1 1
50 483
- -
0.0 6.7
almost 3 years ago 6 days ago
Python R
MIT License GNU Lesser 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).

dada2

Posts with mentions or reviews of dada2. 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 dada2 you can also consider the following projects:

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

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

TCGAbiolinks - TCGAbiolinks

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

MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

drep - Rapid comparison and dereplication of genomes

rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

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

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

seqinr - Biological sequences retrieval and analysis

kraken-biom vs GTDBTk dada2 vs GTDBTk kraken-biom vs MMseqs2 dada2 vs TCGAbiolinks kraken-biom vs atlas dada2 vs MicrobiomeStat kraken-biom vs drep dada2 vs rBLAST kraken-biom vs taxopedia dada2 vs MMseqs2 kraken-biom vs GraphBin2 dada2 vs seqinr
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