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.