- paired-ends: Paired sequences from the two ends of a DNA fragment, mate-pairs and molecular-barcoding.
- align-genus: Alignment to a reference genome within the same genus.
- align-xgenus: Alignment to a reference genome within another genus.
- map: Linkage asserted using a non-sequence based map such as RH, linkage, fingerprint or optical.
- proximity-ligation: Ligation of segments of DNA that were brought into proximity in chromatin (Hi-C and related technologies).
- align-trnscpt: Alignment to a transcript from the same species.
Much less common:
- within-clone: Sequence on both sides of the gap is derived from the same clone, but the gap is not spanned by paired-ends. The adjacent sequence contigs have unknown order and orientation.
- clone-contig: Linkage is provided by a clone contig in the tiling path (TPF). For example, a gap where there is a known clone, but there is not yet sequence for that clone.
Note: if more than one linkage evidence was used, then we cannot convert the runs of Ns appropriately, so you need to make a .sqn file using MakeGapTable.pl and tbl2asn