Where is the documentation for PacBio tool bam2fastx?

Question

[Bharat Iyengar]

I am planning to use bam2fastx tool for converting the BAM files from PacBio sequencing to fastq. (I prefer a command line tool over SMRT link). However, I cannot find any manual for this tool.

The help says that there is an option called --split-barcodes for demultiplexing. However, there is no information about the format to provide the barcodes in. My sequencing data contains ~120 asymmetrically PCR-barcoded samples. How do I split the data into multiple files using this tool?

Answer 1

[GenoMax]

Documentation for the commands can be found in the official SMRTanalysis guide. I don't see any way to specify index sequences so it must be recognizing official PacBio indexes. There is one more page here.

[Bharat Iyengar]

The SMRT link user guide says that the barcodes should be provided in a csv format. Do you think this tool would use the same format?

[GenoMax]

Yes. It is the same tool accessed on the command line.

[Bharat Iyengar]

I tried running --split-barcodes without any argument (not sure if it takes any argument) and it gave an error: subreads.bam has no barcoding data

[Bharat Iyengar]

I just found that there is another application for demultiplexing: lima

[GenoMax]

Did lima work?

[Bharat Iyengar]

Trying. Reading the documentation. Will update.

[rohitsatyam102]

Hi Were you able to demultiplex the PacBio data? If yes how. I am struggling as well.

[Bharat Iyengar]

Yes. I used lima and it worked quite well. However, I am not sure if the SMRT tools package is the same or if they have done major updates.