Galaxy |

VAPOR (version 1.0.2+galaxy3)

Reference sequences:

Select a multisample fasta dataset with reference sequences to base classification on.

Type of sequencing data:

Sequenced reads:

Specify the sequenced reads dataset.

Desired output:

Limit number of reported matches to:

Determines the maximum number of candidate matches sorted by score that will be reported. Set to zero to get all candidate matches reported.

Optional arguments

Optional arguments 0

What it does

VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR works on a fasta file of full-length reference sequences for a given genome segment and a set of sequenced reads, and attempts to retrieve the reference that is closest to the sequenced strain.

sub_sample is not an option here (compared to the tool on GitHub), since you can always build a workflow that preprocesses your reads to a (random) subsample. You can use this output as your reads file for VAPOR.