CLI example

Data generated using the MAS-Seq for single-cell IsoSeq kit on either Sequel IIe or Revio can be downloaded here.

# download HiFi reads for MAS-Seq PBMCs run on Sequel IIe
wget https://downloads.pacbcloud.com/public/dataset/MAS-Seq/DATA-SQ2-PBMC_5kcells/0-CCS/m64476e_220618_014917.hifi_reads.bam

# download MAS adapter fasta
wget https://downloads.pacbcloud.com/public/dataset/MAS-Seq/REF-MAS_adapters/MAS-Seq_Adapter_v1/mas16_primers.fasta

# run skera split to generate segmented reads
skera split m64476e_220618_014917.hifi_reads.bam mas16_primers.fasta segmented.bam

An example of the segmented.bam output can be found here

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