Torrent Browser User Interface Guide

TMAP map2 Options

This page describes the parameters for the TMAP map2 module. The map2 module implements BWA-long / BWASW reads mapping.

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The map2 module is not the current default for TMAP.

Options supported with the TMAP map2 module(all are optional):

Option	Type	Default	Description
--max-seed-hits	INT	1024	The maximum number of hits returned by a seed
--length-coef	FLOAT	5.5	The coefficient of length-threshold adjustment
--max-seed-intv	INT	6	The maximum seeding interval size
--z-best	INT	1	The maximum number of top-scoring nodes to keep on each iteration
--seeds-rev	INT	5	The number of seeds to trigger reverse alignment
--narrow-rmdup	INT	false	Remove duplicates for narrow SA hits
--max-chain-gap	INT	10000	The maximum gap size during chaining
--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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