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.
Software page: https://github.com/B-UMMI/seq_typing
- Input type:
- Output type: None
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.
results/seqtyping/<sample id>: Stores the results of seq_typing in text and tabular format.