Skera splits MAS-Seq 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.

Availability

The latest version can be installed via bioconda package pbskera.

Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer.

Versions

Version 1.2.0: Full changelog here

Input

HiFi Reads

HiFi reads in PacBio BAM format.

Adapters

Adapters in FASTA format.

Execution

Skera split run on HiFi reads in PacBio BAM format:

skera split <movie>.hifi_reads.bam adapters.fasta <movie>.skera.bam

Skera undo:

skera undo <movie>.skera.bam <movie>.undo.bam