Helicobacter pylori virulence factor genotyper

About

This is an experimental genotyper of H. pylori virulence genes: CagA, VacA and OipA.

This tool is shared with the hope that it can be useful, but without any guarantees.

Download

• helpvifag-0.1.2.zip (July 19, 2023) - shared under the zlib/libpng license.

Usage

helpvifag.pl [Options]

Options:

--CagA-nuc-seq SEQ - Use SEQ as CagA nucleotide sequence.

--CagA-aa-seq SEQ - Use SEQ as CagA amino acid sequence.

--VacA-nuc-seq SEQ - Use SEQ as VacA nucleotide sequence.

--OipA-nuc-seq SEQ - Use SEQ as OipA nucleotide sequence.

--CagA-nuc-file FILE - Read CagA nucleotide sequence(s) from FILE.

--CagA-aa-file FILE - Read CagA amino acid sequence(s) from FILE.

--VacA-nuc-file FILE - Read VacA nucleotide sequence(s) from FILE.

--OipA-nuc-file FILE - Read OipA nucleotide sequence(s) from FILE.

--genes-nuc-file FILE - Read gene sequences from FILE (in FASTA format). FILE is used as a wildcard, if it contains * or ?. FILE can be also a zip archive containing FASTA files.

--prokka-file FILE - FILE is a zip-compressed output of PROKKA annotation for one or more samples.

--out-CagA FILE - Write CagA genotypes to tsv FILE.

--out-VacA FILE - Write VacA genotypes to tsv FILE.

--out-OipA FILE - Write OipA genotypes to tsv FILE.

--stats - Print statistics.

--verbose - Verbose output.

--temp-dir DIR - Use DIR for decompressing zip archives ('.' by default).

--use-seq-align - Use seq-align for VacA genotyping.

--use-mafft - Use MAFFT for VacA genotyping.

--quiet - No console output.

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