Balík: kaptive (2.0.8-1)
Odkazy pre kaptive
Zdroje Debian:
Stiahnuť zdrojový balík kaptive:
Správcovia:
- Debian Med Packaging Team (Stránka QA, Konferencia)
- Andreas Tille (Stránka QA)
- Étienne Mollier (Stránka QA)
Externé zdroje:
- Domovská stránka [github.com]
Podobné balíky:
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.
Ostatné balíky súvisiace s balíkom kaptive
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- dep: ncbi-blast
- next generation suite of BLAST sequence search tools
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-biopython
- Python3 library for bioinformatics
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- sug: kaptive-data
- reference data for kaptive for Klebsiella genome assemblies
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- sug: kaptive-example
- example data for kaptive for Klebsiella genome assemblies
Stiahnuť kaptive
Architektúra | Veľkosť balíka | Nainštalovaná veľkosť | Súbory |
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all | 23.6 kB | 110.0 kB | [zoznam súborov] |