Output Files

Segmented BAM files

  • segmented.bam

    Skera outputs a BAM file containing all segmented reads that have sequential leading and trailing adapters based on the order of adapters in the input fasta.

  • segmented.non_passing.bam

    The non_passing.bam file contains the bam records that have adapters found in non-sequential order. This file is necessary for skera undo.

Reports

  • summary.csv

    The summary.csv contains general summary statistics for read segmentation.

  • ligations.csv

    The ligations.csv file contains the counts of all leading and trailing adapter combinations found in all passing and non-passing segments.

  • read_lengths.csv

    The read_lengths.csv file contains the parent HiFi and s-read lengths for all passing segments.

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