.TH PLS2FASTA "1" "July 2015" "pls2fasta 3ca7fe8" "User Commands"
.SH NAME
pls2fasta \- convert plx.h5/bax.h5/fofn files to fasta or fastq files
.SH SYNOPSIS
.B pls2fasta
.I in.bax.h5
.I out.fasta
.RI [ options ]
.SH 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 \fB\-trimByRegion\fR.
.SH OPTIONS
.TP
.I in.bax.h5
Input plx.h5/bax.h5/fofn file.
.TP
.I out.fasta
Output fasta/fastq file.
.TP
.B \-trimByRegion
Trim away low quality regions.
.TP
.B \-maskByRegion
Mask low quality regions with 'N'.
.TP
.BI \-regionTable \0value
Optional HDF file with a \fI\,/PulseData/Regions\/\fP dataset.
.TP
.BI \-minSubreadLength \0value
Do not write subreads less than the specified length.
.TP
.B \-noSplitSubreads
Do not split reads on adapter sequences.
.TP
.B \-holeNumber
Only print this hole number (or list of numbers).
.TP
.B \-fastq
Print in FASTQ format with quality.
.TP
.B \-ccs
Print de novo circular consensus (ccs) sequences
.TP
.B \-lineLength \0value
Specify fasta/fastq line length
.TP
.BI \-minReadScore \0value
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.
.TP
.B \-best
If a ccs sequence exists, print this.
Otherwise, print the longest subread.
This does not support fastq.
.SH SEE ALSO
.BR blasr (1)
.BR loadPulses (1)
.BR samFilter (1)
.BR samtoh5 (1)
.BR samtom4 (1)
.BR sawriter (1)
.BR sdpMatcher (1)
.BR toAfg (1)