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Alignment file	Alignment tools	Downloading and Installing SHORE
FAQ	FlatRead	Frequently Asked Questions
Frequently asked questions	Genomemapper	IndexFolder
LaneFolder	LengthFolder	Main Page
Map.list	MapList	NewPage
ReadFolder	Read file	Reads 0.fl
RunFolder	Running SHORE for the First Time - A Quick Guide	Running SHORE for the first time - A Quick Guide
SHORE Documentation	SHORE File Formats	SHORE Overview
SHORE Subprograms	SHORE file formats	SHORE main program
SHORE subprograms	SHORE v0.7 file formats	SampleFolder
Shore 2dex	Shore annotate region	Shore binom test
Shore compress	Shore consensus	Shore convert
Shore correct4pe	Shore count	Shore coverage
Shore directory	Shore idtrans	Shore import
Shore mapdisp	Shore mapflowcell	Shore merge
Shore methyl	Shore mg	Shore mtc
Shore peak	Shore preprocess	Shore qVar
Shore qvar	Shore ranksim	Shore sort
Shore srna	Shore structure	Shore tagstats
Subprogram	Subprograms	Supported Short Read Aligners
System Requirements	Temporary files	The libshore C++ Library
Using SHORE with MPI

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