Segments #

Modern sequencers, particularity Illumina sequencers can read multiple times from one (amplified) DNA molecule, producing multiple ‘segments’ that together form a ‘molecule’.

The user’s define the available segments in the input-section, common names are ‘read1’, ‘read2’ (for paired-end reads) and ‘index1’, ‘index2’ (for dual-indexed libraries).

These are then commonly available to steps taking a segment or a source option. Often there is the option to work on all all defined segments at once by using the ‘All’ ‘segment/source’.