Alessia
2017-11-28
<p>This dataset includes all the databases/datasets queried by YAMP (https://github.com/alesssia/YAMP). This dataset has been created to help the users to get started with YAMP, and to save them from the hassle of collecting and downloading the data from different sources.</p>
<p>More in details, this dataset contains:</p>
<ul>
<li>a FASTA file listing the adapter sequences to remove in the trimming step. This file is usually provided within the BBmap installation (https://sourceforge.net/projects/bbmap, version 37.68). </li>
<li>two FASTA files describing synthetic contaminants (sequencing_artifacts.fa.gz and phix174_ill.ref.fa.gz). These files are usually provided within the BBmap installation (https://sourceforge.net/projects/bbmap, version 37.68). </li>
<li>a FASTA file provided by Brian Bushnell for removing human contamination (described here: http://seqanswers.com/forums/showthread.php?t=42552). Please note that this file should be indexed beforehand. This can be done using BBMap, using the following command: `bbmap.sh -Xmx24G ref=hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz`. </li>
<li>the BowTie2 database file for MetaPhlAn2. This file is usually provided within the MetaPhlAn2 installation (version 2.6.0)</li>
<li>the ChocoPhlAn and UniRef (Uniref50, Uniref90) databases, downloaded directly by HUMAnN2 (version 0.9.9), as explained here: https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-5-download-the-databases</li>
</ul>
<p><br>
</p>
https://doi.org/10.5281/zenodo.1068229
oai:zenodo.org:1068229
Zenodo
https://doi.org/10.5281/zenodo.1068228
info:eu-repo/semantics/openAccess
Creative Commons Attribution Share Alike 4.0 International
https://creativecommons.org/licenses/by-sa/4.0/legalcode
metagenomics, workflow,
Data for YAMP (https://github.com/alesssia/YAMP)
info:eu-repo/semantics/other