NAME

       yanagiba - Filters low quality Oxford Nanopore reads basecalled with Albacore

DESCRIPTION

       usage: yanagiba [-h] -i INFILE [-s SUMMARYFILE] [-o OUTFILE] [-l MINLEN]

              [-q MINQUAL] [--headtrim HEADTRIM] [--tailtrim TAILTRIM] [-u]

       Filter  and slice Nanopore reads which have been basecalled with Albacore.  Takes fastq.gz
       and an Albacore summary file.

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

       -i INFILE, --infile INFILE
              Input fastq.gz file.

       -s SUMMARYFILE, --summaryfile SUMMARYFILE
              Albacore summary file with header row.

       -o OUTFILE, --outfile OUTFILE
              Write filtered reads to this file in .bgz format.

       -l MINLEN, --minlen MINLEN
              Exclude reads shorter than this length. Default: 0

       -q MINQUAL, --minqual MINQUAL
              Minimum quality score to retain a read. Default: 10

       --headtrim HEADTRIM
              Trim x bases from beginning of each read. Default: 0

       --tailtrim TAILTRIM
              Trim x bases from end of each read. Default: None

       -u, --forceunique
              Enforce unique reads. Only store first instance of a read from  fastq  input  where
              readID occurs multiple times.

AUTHOR

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