Galaxy | Tool Preview

FROGS TSV_to_BIOM (version 2.0.0)
Your FROGS abundance TSV file. Take care to keep original column names.
TSV file describing multi_hit blast results.
If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file.
/repository/static/images/525e78406276b403/static%2Fimages%2FFROGS_logo.png

What it does

This tool converts a TSV file in a BIOM file.

Inputs

Abundance file:

The table with abundances each cluster in each sample and other details conerning the cluster (format TSV).

Authorised column names : rdp_tax_and_bootstrap, blast_taxonomy, blast_subject, blast_perc_identity, blast_perc_query_coverage, blast_evalue, blast_aln_length, seed_id, seed_sequence, observation_name, observation_sum

Multiple affiliation file:

The file that stores the multiple blast hits.

Outputs

Abundance file:

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

Sequence file [optional]:

By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in FASTA format. For this option, be sure that your TSV file contains the seed_sequence column.

How it works

FROGS TSV_to_BIOM detects any metadata (columns before "observation_name") and names of samples (columns after "observation_sum").

Then it reconstructs the BIOM abundance file : for each "observation_name" it adds the associated metadata and the count of samples.

If blast_taxonomy is included in metadata and if blast_subject is equal to "multi-subject", it parses multi_hit TSV file. Then it extracts the list of blast_affiliations that contains the non ambiguous blast_taxonomy.

Advices

This tool is usefull if you have modified your abundance TSV file and that you want to generate rarefaction curve or sunburst with the FROGS affiliation_stat tool.

If you modify your abundance TSV file

  • -do not modify column names
  • -do not remove columns
  • -take care to choose a taxonomy available in your multi_hit TSV file
  • -if you delete lines of the multi_hit file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file.
  • -if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_hit 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., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA , http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf

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