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)

pls2fasta 3ca7fe8                                   July 2015                                       PLS2FASTA(1)