Analysis software

List of software tools for bioinformatics analysis of OM data

Key feature	Tool	Description	URL	Ref
Data simulation	OMSim	A tool for producing synthetic Bionano optical maps	OMTools	[1]
	BMSIM	A tool for producing and mimicking real Bionano molecules	BMSIM	[2]
Data correction	cOMet	A tool for raw map error correction using k-mer seeds	cOMet	[3]
	Elmeri	A tool for raw map error correction using spaced-mer seeds	Elmeri	[4]
Map alignment	RefAligner	An aligner for map alignment owned by Bionano Genomics using a dynamic programming framework	RefAligner	NA
	OMBlast	An aligner for map alignment using a modified seed-and-extend method	OMBlast	[5]
	OMMA	An aligner for multiple map alignment in a population-scale study	OMMA	[6]
	Maligner	An aligner for raw map alignment based on a dynamic programming framework for large eukaryotic genomes and an indexed method for identifying discordances in the reference	Maligner	[7]
	OPTIMA	An aligner for whole genome alignment using a novel seed-and-extend global alignment method	OPTIMA	[8]
Genome assembly	Assembler	An assembler for de novo map assembly owned by Bionano Genomics	Assembler	NA
	Novo&Stitch	A tool for assembly reconciliation and scaffolding	Novo&Stitch	[9]
	BiSCoT	A tool for scaffold contiguity improvement based on map alignment	BiSCoT	[10]
Assembly evaluation	BionanoAnalyst	A tool for reporting and visualizing potential errors in the genome assemblies based on discordances in the alignment	BionanoAnalyst	[11]
	misSEQuel	A tool for reporting and resolving mis-assemblies using optical maps and paired-end reads	misSEQuel	[12]
SV detection	OMSV	A tool for SV detection based on map alignment from OMBlast and RefAligner using a complete error model	OMSV	[13]
	Structome	A tool for SV detection using Bionano Irys data and map alignment	Structome	NA
Data management and visualization	IrysView	A tool bundled with the Bionano Irys platform for data analysis, data management and visualization on a window system	IrysView	NA
	Bionano Access	A tool package bundled with the Bionano Saphyr platform for data analysis, data management and visualization on multiple operating systems	Bionano Access	NA
	MapOptics	A tool for viewing comparisons of in silico maps, empirical optical maps, and hybrid scaffolds	MapOptics	[14]
	OMTools	A toolkit for data processing, map alignment and visualization	OMTools	[15]
Pipeline wrapper	runBNG	A wrapper of Bionano IrysSolve Scripts package for data processing and analysis on Linux systems	runBNG	[16]
	Irys-scaffolding	A refined pipeline for genome assembly based on Bionano RefAligner and Assembler	Irys-scaffolding	[17]
	OMWare	A refined pipeline for genome assembly based on Bionano RefAligner and Assembler	OMWare	[18]