seq_typing

Purpose

Seq_typing is a software that determines the type of a given sample using a read mapping approach against a set of reference sequences. Sample’s reads are mapped to the given reference sequences and, based on the length of the sequence covered and it’s depth of coverage, seq_typing decides which reference sequence is more likely to be present and returns the type associated with such sequences.

Note

Software page: https://github.com/B-UMMI/seq_typing

Input/Output type

  • Input type: FastQ
  • Output type: None

Parameters

  • referenceFileO: Fasta file containing reference sequences. If more than one file is passed via the ‘referenceFileH parameter, a reference sequence for each file will be determined.
  • referenceFileH: Fasta file containing reference sequences. If more than one file is passed via the ‘referenceFileO parameter, a reference sequence for each file will be determined.

Published results

  • results/seqtyping/<sample id>: Stores the results of seq_typing in text and tabular format.

Published reports

None.

Default directives

  • cpus: 4
  • memory: 4GB
  • container: ummidock/seq_typing
  • version: 0.1.0-1

Advanced

Reports JSON

typing:
  • seqtyping: <typing result>