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fa2dna - format fasta database for use with ANFO


fa2dna [ option | file ... ]


fa2dna reads one or more files in fasta format and reformats them into a database suitable
for anfo(1). The input file(s) can contain more than one sequence, and each sequence can
be broken up into multiple contigs by a stretch of Ns. All IUPAC ambiguity codes are
fully supported.


-V, --version
Print version number and exit.

-o file, --output file
Write output to file.file should end in .dna, because anfo and some downstream
tools might stumble over a different extension. Default is the genome name with
the .dna extension.

-m N, --maxn N
Sets the maximum number of Ns to be interpreted as IUPAC ambiguity codes to N; any
longer stretch is interpreted as separing contigs. Default is 2.

-g name, --genome name
Sets the genome name to name. This name is stored in the output file and will be
used by anfo to identify the matched genome in its output. The genome should be a
prefix of the output file name to allow downstream tools to find it. The name
should be short, but unique, something like "hg18" or "pt2" for human or chimpanzee
genomes would work fine.

-d text, --description text
Adds text as description to the metadata. This is purely informational.

-v, --verbose
Causes a progress indicator to be printed.

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