Galaxy |

mash screen (version 2.3+galaxy3)

Single or Paired-end reads:

Select between paired and single end data

Select first set of reads:

Specify dataset with forward reads

Select second set of reads:

Specify dataset with reverse reads

Select queries from your history or use one from a tool data table?:

queries:

'Winner takes all' to remove redundancy in the result:

If this option is not enabled, every matching strain from the same species of the reference database is reported in the result.

Minimum identity to report:

Maximum p-value to report:

What it does

Determine how well query sequences are contained within a pool of sequences. The queries must be formatted as a single Mash sketch file (.msh), created with the mash sketch command. The <pool> files can be contigs or reads, in fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from standard input. The <pool> sequences are assumed to be nucleotides, and will be 6-frame translated if the <queries> are amino acids. The output fields are [identity, shared-hashes, median-multiplicity, p-value, query-ID, query-comment], where median-multiplicity is computed for shared hashes, based on the number of observations of those hashes within the pool.