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

        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)

       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

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

   optionalarguments:-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'

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