vaporup 1.0.3

Vapor is a tool for classification of Influenza samples from short read sequence data, which can be apllied also to other viruses.

VaporUp is an actively developed and maintained version of Vapor, a tool for classification of Influenza samples from raw short read sequence data. From a fasta file of (preferably thousands of) full-length viral reference sequences for a given segment, and a set of reads, VaporUp attempts to identify the reference that is closest to the sample strain.

Example usage

Test inputs are provided in the tests folder of the development repo, which also has more detailed usage instructions.

With VaporUp installed you can run:

vapor.py -fq tests/test_reads.fq -fa tests/HA_sample.fa

which should yield:

0.9782480893592005  186719.0    1701    109.77013521457965  1000    >cds:ADO12563 A/Chile/3935/2009 2009/07/07 HA H1N1 Human

Where the tab-delimited fields correspond to: approximate fraction of query bases found in reads; total score; query length; mean score; number of reads surviving culling; query description.

Acknowledgments

Original author of VAPOR: Joel Southgate