Ubuntu
kaptive package

kaptive 2.0.3-1 source package in Ubuntu

Changelog

kaptive (2.0.3-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Standards-Version: 4.6.1 (routine-update)
  * Refresh patch blastdb_4.
  * Delete patch extend_bad_versions: applied upstream.
  * Delete fix-which-error-output.patch: applied upstream.
    Thanks to Andreas Tille for the mass patch forwarding.
  * d/rules: dynamically adjust version number of directory in cleanup command.

 -- Étienne Mollier <email address hidden>  Thu, 02 Jun 2022 22:31:31 +0200

Upload details

Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
all
Section:
misc
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section

Builds

Kinetic: [FULLYBUILT] amd64

Downloads

File Size SHA-256 Checksum
kaptive_2.0.3-1.dsc 2.2 KiB 817c8b7a9ab49c7a9cac3fae3d3349cdceda8ab1372079e504d9421347643fa0
kaptive_2.0.3.orig.tar.gz 14.5 MiB 9bc68b52dce17d6a935e9738a71debf1f236834f5d2461dbc981cf412a236076
kaptive_2.0.3-1.debian.tar.xz 6.1 KiB 68e5df60de1d3e9ebcf321d588d334eab2d7f4eaf1528cfaf1cf044622a27394

Available diffs

No changes file available.

Binary packages built by this source

kaptive: 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.

kaptive-data: No summary available for kaptive-data in ubuntu kinetic.

No description available for kaptive-data in ubuntu kinetic.

kaptive-example: 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.