Provided by: blasr_5.3+0-2_amd64
pls2fasta - convert plx.h5/bax.h5/fofn files to fasta or fastq files
pls2fasta in.bax.h5 out.fasta [options]
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.
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.
blasr(1) loadPulses(1) samFilter(1) samtoh5(1) samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)