Skera splits arrayed PacBio HiFi reads at adapter positions generating segmented reads (S-reads). For each input/parent read (e.g. HiFi) skera will create multiple bam records, one for each S-read. A parent read can contain many S-reads. Skera has two major functions, split and undo. Skera undo reconstitutes the original parent read from input S-reads.
skera can be installed via the bioconda.
Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer.
Version 0.1.0: Full changelog here
HiFi reads in PacBio BAM format.
Adapters in FASTA format.
Skera split run on HiFi reads in PacBio BAM format:
skera split <movie>.hifi_reads.bam adapters.fasta <movie>.skera.bam
skera undo <movie>.skera.bam <movie>.undo.bam