Concepts on mbf-fastq-processor documentation

Mon, 01 Jan 0001 00:00:00 +0000

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’.

Mon, 01 Jan 0001 00:00:00 +0000

Source #

When a step refers to a ‘source’ (instead of a segment), it means that it can read from segment, a segment’s name (e.g. “name:read1”) or a (location/string) tag value (e.g. “tag:mytag”)

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Step #

A step is one coherent manipulation of the FASTQ stream and it’s associated data.

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Tag / Label #

A tag is a piece of molecule derived data that one step in the pipeline produces, and others may use (or output).

Tags have types: - Location+Sequence (which may loose their location data) - Sequence-only - numeric - boolean

For example ExtractIUPAC produces a ’location’ tag.

That location tag then allows filtering for it’s presence using FilterByTag, cutting the segment at it’s location using TrimAtTag or replacing it’s sequence with LowercaseTag.