Where is the documentation for PacBio tool bam2fastx?
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3.3 years ago

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?

pacbio sequencing • 1.7k views
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3.3 years ago
GenoMax 120k

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.

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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?

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

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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

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

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Did lima work?

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Trying. Reading the documentation. Will update.

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