FASTAQ-TO_FASTA

NAME

fastaq_to_fasta - Converts a variety of input formats to nicely formatted FASTA format

DESCRIPTION

usage: fastaq_to_fasta [options] <infile> <outfile>

Converts a variety of input formats to nicely formatted FASTA format

positional arguments:

infile

Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip

outfile

Name of output file

options:

-h, --help

show this help message and exit

-l LINE_LENGTH, --line_length LINE_LENGTH

Number of bases on each sequence line of output file. Set to zero for no linebreaks in sequences [60]

-s, --strip_after_whitespace

Remove everything after first whitespace in every sequence name

-u, --check_unique

Die if any of the output sequence names are not unique