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Source: kaptive
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
Étienne Mollier <emollier@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3,
python3-setuptools,
python3-biopython <!nocheck>,
debhelper
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/kaptive
Vcs-Git: https://salsa.debian.org/med-team/kaptive.git
Homepage: https://github.com/katholt/Kaptive
Rules-Requires-Root: no
Package: kaptive
Architecture: all
Depends: ${python3:Depends},
${misc:Depends},
python3-biopython,
ncbi-blast+
Suggests: kaptive-data,
kaptive-example
Description: obtain information about K and O types for Klebsiella genome assemblies
Kaptive reports information about K and O types for Klebsiella genome
assemblies.
.
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
coverage).
* 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
FASTA file.
* 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.
Package: kaptive-data
Architecture: all
Depends: ${misc:Depends}
Enhances: kaptive
Multi-Arch: foreign
Description: reference data for kaptive for Klebsiella genome assemblies
Kaptive reports information about K and O types for Klebsiella genome
assemblies.
.
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
coverage).
* 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
FASTA file.
* 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 a reference database. Its not necessarily used
to run kaptive since you can use your own database.
Package: kaptive-example
Architecture: all
Depends: ${misc:Depends}
Enhances: kaptive
Multi-Arch: foreign
Description: example data for kaptive for Klebsiella genome assemblies
Kaptive reports information about K and O types for Klebsiella genome
assemblies.
.
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
coverage).
* 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
FASTA file.
* 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.
|
