Torrent Browser User Interface Guide

TMAP map3 Options

This page describes the parameters for the TMAP map3 module. The map 3 module implements a s implified SSAHA, based on a k-mer lookup table.

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The map 3 module is not the current default for TMAP.

Options supported with the TMAP map 3 module(all are optional):

Option	Type	Default	Description
--seed-length	INT	-1	The k-mer length to seed CALs (-1 to disable)
--max-seed-hits	INT	20	The maximum number of hits returned by a seed
--hit-frac	FLOAT	0.2	The fraction of seed positions that are under the maximum
--seed-step	INT	8	Thenumber of bases to increase the seed for each seed increase iteration (-1 to disable)
--hp-diff	INT	0	The single homopolymer error difference for enumeration
--fwd-search	Boolean	false	Use forward search instead of a reverse search
--skip-seed-frac	FLOAT	0.2	The fraction of a seed to skip when a lookup succeeds
--min-seq-length	INT	-1	The minimum sequence length to examine (-1 to disable)
--max-seq-length	INT	-1	The maximum sequence length to examine(-1 to disable)

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