Table 1.

Summary of overlap tools output formats, associated pipelines and availability

Software	Algorithm features	Associated assembly tools	Output	Availability
BLASR	FM-Index, anchor clusters	PBcR	SAM alignment, other proprietary formats (overlap regions)	https://github.com/PacificBiosciences/ blasr
DALIGNER	Cache efficient k-mer sort (radix) and merge	DAZZLER, MARVEL, FALCON	Local Alignments, LAS format (alignment tracepoints)	https://github.com/thegenemyers/ DALIGNER
MHAP	MinHash	PBcR, Canu	MHAP output format (overlap regions)	https://github.com/marbl/MHAP
GraphMap	Gapped q-gram (spaced seeds), colinear clustering	Ra	SAM alignment, MHAP output format (overlap regions)	https://github.com/isovic/GraphMap
Minimap	Minimizer colinear clustering	Miniasm	PAF (overlap regions)	https://github.com/lh3/Minimap