NAME

       to_fasta.py - Remove adapters and collapse reads from FASTQ to FASTA

DESCRIPTION

       usage: to_fasta.py [-h] [-3 SEQ] [-5 SEQ] [--trim-5p BP] [--trim-3p BP]

              [--seed-5p BP] [--seed-3p BP] [-m BP] [-x BP] [-s] [-B] [-a] FASTQ

       Remove adapters and collapse reads from FASTQ to FASTA

   positional arguments:
       FASTQ  including stdin or compressed file {zip,gz,tar,bz}

   optional arguments:
       -h, --help
              show this help message and exit

       -3 SEQ 3'adapter sequence

       -5 SEQ 5'adapter sequence

       --trim-5p BP
              trim specified number of bases from 5'ends

       --trim-3p BP
              trim specified number of bases from 3'ends

       --seed-5p BP
              5' adapter match length in bp (default: 7)

       --seed-3p BP
              3' adapter match length in bp (default: 7)

       -m BP  minimum read length in bp (default: 16)

       -x BP  maximum read length in bp (default: 36)

       -s     sensitive adapter search with 1 mismatch (default: off)

       -B     only print the reads with both 5' and 3' adapter matches

       -a     print all reads with and without adapter matches if the reads are in the range specified with '-m'
              and '-x'

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

to_fasta.py 1.1                                    March 2020                                     TO_FASTA.PY(1)