handle_fasta: Handles fasta files
In ojcharles/hsvdrg: Herpes Simplex Virus 1 and 2 Drug Resistance Genotyping
Description
Usage
Arguments
Details
Value
Description
Decides whether the provided fasta file is, whole genome Merlin aligned/ assembled,
Whole genome other, or only covers a fraction of the genome.
If not WG Merlin type, then it aligns using MAFFT –add –keeplength.
Usage
1
handle_fasta(fasta_in, fasta_out, fasta_ref)
Arguments
fasta_in
Path to the input file
fasta_out
filename of fasta alignment produced
fasta_ref
the Merlin reference fasta file
Details
Then converts to VCF using snp-sites
Value
vcf file and fasta alignment
ojcharles/hsvdrg documentation built on Jan. 19, 2021, 2:02 p.m.
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Description Usage Arguments Details Value
Description
Decides whether the provided fasta file is, whole genome Merlin aligned/ assembled, Whole genome other, or only covers a fraction of the genome. If not WG Merlin type, then it aligns using MAFFT –add –keeplength.
Usage
1 | handle_fasta(fasta_in, fasta_out, fasta_ref)
|
Arguments
fasta_in |
Path to the input file |
fasta_out |
filename of fasta alignment produced |
fasta_ref |
the Merlin reference fasta file |
Details
Then converts to VCF using snp-sites
Value
vcf file and fasta alignment
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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