What it does

Converts a BIOM file in TSV file.

Inputs

Abundance file:

The abundance of each cluster in each sample (format BIOM).

Sequence file [optional]:

The sequences (format FASTA).

Outputs

Abundance file:

The abundance of each cluster in each sample and theirs metadata (format TSV).

If you add the sequences file, this information is added for each cluster.

Multiple affiliation file:

If you have used FROGS affiliation on your data, each OTU can have several affiliations: several alignments with same score on reference database. The multiple affiliation file contains details on these possibles affiliations (format TSV).

How it works

FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the abundance, and extract the detailed abundance for each sample. Finally it will write all these fields separated by tabulation in the TSV file.

Advices

This output tsv file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more OTU, use FROGS Filters to extract for example the most abundant OTU before converting your BIOM abundance table in TSV file.

Contact

Contacts: frogs@inra.fr

Repository: https://github.com/geraldinepascal/FROGS

Please cite the FROGS Publication: Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France, http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf

Depending on the help provided you can cite us in acknowledgements, references or both.