CLI example

Data generated using the Kinnex kits can be downloaded here. Different Kinnex kits offer different concatenation factors: 16-fold for Kinnex single-cell RNA kit, 12-fold for Kinnex 16S rRNA kit, 8-fold for Kinnex full-length RNA kit. Choose the appropriate MAS/Kinnex adapter set accordingly.

# download HiFi reads 
wget https://downloads.pacbcloud.com/public/dataset/MAS-Seq/DATA-Revio-Kinnex-HG002-10x5p/0-CCS/m84039_240124_190648_s3.hifi_reads.bcM0002.bam

# download MAS/Kinnex adapter fasta for the Kinnex single-cell RNA kit (which uses a 16-fold concatenation)
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 m84039_240124_190648_s3.hifi_reads.bcM0002.bam mas16_primers.fasta segmented.bam

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

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