NAME

       pls2fasta - convert plx.h5/bax.h5/fofn files to fasta or fastq files

SYNOPSIS

       pls2fasta in.bax.h5 out.fasta [options]

DESCRIPTION

       Although  fasta  files  are  provided  with every run, they are not trimmed nor split into
       subreads. This program takes  additional  annotation  information,  such  as  the  subread
       coordinates  and  high  quality  regions, and uses them to create fasta sequences that are
       substrings of all bases called. Most of the time, you will want to trim low quality reads,
       so you should specify -trimByRegion.

OPTIONS

       in.bax.h5
              Input plx.h5/bax.h5/fofn file.

       out.fasta
              Output fasta/fastq file.

       -trimByRegion
              Trim away low quality regions.

       -maskByRegion
              Mask low quality regions with 'N'.

       -regionTable value
              Optional HDF file with a /PulseData/Regions dataset.

       -minSubreadLength value
              Do not write subreads less than the specified length.

       -noSplitSubreads
              Do not split reads on adapter sequences.

       -holeNumber
              Only print this hole number (or list of numbers).

       -fastq Print in FASTQ format with quality.

       -ccs   Print de novo circular consensus (ccs) sequences

       -lineLength  value
              Specify fasta/fastq line length

       -minReadScore value
              Minimum  read  score to print a read.  The score is a number between 0 and 1000 and
              represents the expected accuracy percentage * 10. A typical value would be  between
              750 and 800.  This does not apply to ccs reads.

       -best  If  a ccs sequence exists, print this.  Otherwise, print the longest subread.  This
              does not support fastq.

SEE ALSO

       blasr(1)  loadPulses(1)  samFilter(1)  samtoh5(1)  samtom4(1)  sawriter(1)   sdpMatcher(1)
       toAfg(1)