# 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.

## 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.

None.

## Default directives¶

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

typing:
• seqtyping: <typing result>