SMRT Tools

SMRT Tools for manipulating PacBio data.

Notes:

• SMRT Tools comes bundled with the SMRT Link package.
• Full documentation for SMRT Tools v6.0.0 can be found here: https://www.pacb.com/wp-content/uploads/SMRT_Tools_Reference_Guide_v600.pdf.

Converting RSII bax.h5 data into Sequel unaligned BAM / XML format

SMRT Tools was designed to operate on data from the PacBio Sequel instrument. In order to use legacy RSII instrument data, it needs to be converted to one of these formats.

RSII bax.h5 to PacBio BAM:

# Make a BAM file for each movie.
bax2bam -o ${PREFIX} $( find . -name "*.bax.h5" )

RSII bax.h5 to PacBio XML Data set:

# Make an XML file for each movie.
bax2bam -o ${PREFIX}  $( find . -name "*.bax.h5" )
dataset create ${PREFIX}.subreadset.xml ${PREFIX}.subreads.bam

Note: The --output-xml option of bax2bam does not appear to do anything.

Converting PacBio BAM to Fastq/Fasta

Sometimes the BAMs need to be converted to Fastq or Fasta.

Fastq:

bam2fastq -o ${PREFIX} ${PREFIX}.subreads.bam

Fasta:

bam2fasta -o ${PREFIX} ${PREFIX}.subreads.bam

Converting PacBio XML Data sets to Fastq/Fasta

Fastq:

bam2fastq -o ${PREFIX} ${PREFIX}.subreadset.xml

Fasta:

bam2fasta -o ${PREFIX} ${PREFIX}.subreadset.xml