atlas VS kraken-biom

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

atlas

ATLAS - Three commands to start analyzing your metagenome data (by metagenome-atlas)
metagenomics Annotation Snakemake Assembly genomic-binning functional-annotation taxonomic-classifications
Source Code
metagenome-atlas.github.io
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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
Source Code
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atlas kraken-biom
2 1
346 43
1.2% -
9.3 0.0
3 months ago about 2 years ago
Python Python
BSD 3-clause "New" or "Revised" License MIT License
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atlas

Posts with mentions or reviews of atlas. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-08-23.

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 atlas and kraken-biom you can also consider the following projects:

pypsa-eur - PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

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

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

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

zarp - The Zavolab Automated RNA-seq Pipeline

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

chipseq-smk-pipeline - ChIP-Seq processing pipeline on snakemake

drep - Rapid comparison and dereplication of genomes

eggnog-mapper - Fast genome-wide functional annotation through orthology assignment

bioinformatics - :microscope: Path to a free self-taught education in Bioinformatics!

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

atlas vs pypsa-eur kraken-biom vs GTDBTk atlas vs GraphBin2 kraken-biom vs MMseqs2 atlas vs zarp kraken-biom vs dada2 atlas vs chipseq-smk-pipeline kraken-biom vs drep atlas vs eggnog-mapper kraken-biom vs GraphBin2 atlas vs bioinformatics kraken-biom vs taxopedia