Kaptive reports information about K and O types for Klebsiella genome
Given a novel genome and a database of known loci (K or O), Kaptive will
help a user to decide whether their sample has a known or novel locus.
It carries out the following for each input assembly:
* BLAST for all known locus nucleotide sequences (using blastn) to
identify the best match ('best' defined as having the highest
* Extract the region(s) of the assembly which correspond to the BLAST
hits (i.e. the locus sequence in the assembly) and save it to a
* BLAST for all known locus genes (using tblastn) to identify which
expected genes (genes in the best matching locus) are present/missing
and whether any unexpected genes (genes from other loci) are present.
* Output a summary to a table file.
In cases where your input assembly closely matches a known locus,
Kaptive should make that obvious. When your assembly has a novel type,
that too should be clear. However, Kaptive cannot reliably extract or
annotate locus sequences for totally novel types - if it indicates a
novel locus is present then extracting and annotating the sequence is up
to you! Very poor assemblies can confound the results, so be sure to
closely examine any case where the locus sequence in your assembly is
broken into multiple pieces.
This package contains some example data.
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Install this software package
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