kaptive 2.0.4-1 source package in Ubuntu
Changelog
kaptive (2.0.4-1) unstable; urgency=medium * Fix watch file * New upstream version * Build-Depends: s/python3-all/python3/ since kaptive.py is just a user application * Add usr/lib to kaptive.install * Fix lintian-overrides -- Andreas Tille <email address hidden> Sun, 27 Nov 2022 21:22:44 +0100
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 | Published | Component | Section | |
---|---|---|---|---|
Mantic | release | universe | misc | |
Lunar | release | universe | misc |
Downloads
File | Size | SHA-256 Checksum |
---|---|---|
kaptive_2.0.4-1.dsc | 2.1 KiB | d8aa53a2252de92cada0cb388cbe3703b09b1ea5d91415b4c074a027b6392e1d |
kaptive_2.0.4.orig.tar.gz | 14.5 MiB | c846e1599a183498c8eb060ec15e4084b3f5a5fe708f90a1d0c3ca07d601ad25 |
kaptive_2.0.4-1.debian.tar.xz | 6.5 KiB | 0441d478193e644b2fac24fcb25d576cf9eb6fb4d60054f7ea2aa9f2868a24c9 |
Available diffs
- diff from 2.0.3-2 to 2.0.4-1 (2.0 KiB)
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: 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.
- 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.