Table 1 Hierarchy of assembly data types
From: Hawkeye: an interactive visual analytics tool for genome assemblies
Data type | Description |
|---|---|
Scaffold (100 kb to 10 Mb) | Layout of potentially nonoverlapping contigs based on mate-pair information, ideally spanning entire chromosomes or replicons |
Contig (5 kb to 500 kb) | Layout of overlapping reads with a consensus sequence |
Mate-pair (2 kb to 100 kb) | Pair of end-sequenced reads with a known orientation and separation |
Read (0.5 kb to 1.0 kb) | Base-calls and quality scores assigned to a chromatogram |
Chromatogram (4× 10,000 time points) | Signal data from a sequencing reaction of a physical piece of DNA |