Pakiet: kaptive (2.0.8-1)
Odnośniki dla kaptive
Zasoby systemu Debian:
- Raporty o błędach
- Developer Information
- Dziennik zmian w systemie Debian
- Informacje nt. praw autorskich
- Śledzenie łatek systemu Debian
Pobieranie pakietu źródłowego kaptive:
Opiekunowie:
- Debian Med Packaging Team (Strona QA, Archiwum e-mail)
- Andreas Tille (Strona QA)
- Étienne Mollier (Strona QA)
Zasoby zewnętrzne:
- Strona internetowa [github.com]
Podobne pakiety:
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.
Inne pakiety związane z kaptive
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- dep: ncbi-blast
- next generation suite of BLAST sequence search tools
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- dep: python3
- Interaktywny, wysokopoziomowy i obiektowy język programowania (domyślna wersja Python 3)
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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
Pobieranie kaptive
Architektura | Rozmiar pakietu | Rozmiar po instalacji | Pliki |
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all | 23,6 KiB | 110,0 KiB | [lista plików] |