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SpoTyping (version 2.1+galaxy2)
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SpoTyping is a software for predicting spoligotype from sequencing reads, complete genomic sequences and assembled contigs.

Input:

  • Fastq file - if paired end data is used, you may choose to concatenate paired reads into a single input (e.g. using the cat tool)
  • Fasta file of a complete genomic sequence or assembled contigs of an isolate (with --seq option)

Note on input size: In swift mode the sampling threshold is reached in approximately 30x coverage when using paired end sequencing of a M. tuberculosis genome.

Output:

Count of hits from BLAST result for each spacer sequence and predicted spoligotype in the format of binary code and octal code.

Options:

--noQuery Avoid querying the SITVIT online service to describe the prevalance of the reported spoligotype.

--seq Set this if input is a fasta file that contains only complete genomic sequence or assembled contigs from an isolate. [Default is off]

-s SWIFT, --swift=SWIFT Swift mode, either "on" or "off" [Default: on] - swift mode samples 250 million bases to use for spoligotyping

--sorted Set if input reads are sorted relative to positions on a reference genome. If reads are sorted and swift mode is used, swift mode's sampling is adjusted to sample reads across positions in the genome evenly.

--filter Filter reads such that:

  1. Leading and trailing 'N's would be removed.
  2. Any read with more than 3 'N's in the middle would be removed.
  3. Any read with more than 7 consecutive bases identical would be trimmed/filtered out given the length of the flanking regions.

Got weird spoligotype prediction?

Sequencing throughput is very low (<40Mbp, for example): SpoTyping may not be able to give accurate prediction due to the relatively low read depth.

Interpreting the spoligotype

The binary or octal spoligotype can be used to look up lineage information using a service like TB Lineage.

SITVIT reports

Optionally a report on the detected spoligotype can be retrieved from the SITVIT database. If such a report is requested it can also be illustrated as a (PDF format) plot.