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BAM

The prefix.bam file contains clipped records, annotated with barcode tags, that passed filters.

Read group

Each barcode pair is represented by one read group @RG header line, with the DS tag containing optionally those items

Key Value spec Value example
BarcodeFile Name of the Fasta file containing the sequences of the barcodes used. pacbio_384_barcodes.fasta
BarcodeHash The MD5 hash of the contents of the barcoding sequence file, as generated by the md5sum commandline tool. 0a294bb959fc6c766967fc8beeb4d88d
BarcodeCount The number of barcode sequences in the Barcode File. 384
BarcodeMode Experimental design of the barcodes. Must be Symmetric/Asymmetric/Tailed or None. Symmetric
BarcodeQuality The type of value encoded by the bq tag. Must be Score/Probability/None. Probability

Read tags

Tag Type Description
bc B,S Barcode pair indices, integer codes represent 0-based position in the FASTA file of barcodes
bq i Barcode score / quality, normalized between 0 and 100
bl Z Barcode sequence clipped from leading end
bt Z Barcode sequence clipped from trailing end
ql Z Qualities of barcode bases clipped from leading end, stored as a FASTQ string
qt Z Qualities of barcode bases clipped from trailing end, stored as a FASTQ string
bx B,i Pair of clipped barcode sequence lengths

DataSet

One DataSet, SubreadSet or ConsensusReadset, is generated per output BAM file.

PBI

One PBI file is generated per output BAM file.


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