Currently, there is no unified file formats for optical mapping data. The OMTools package provides support to format conversion of most known formats of optical mapping data and alignment results.
Here is a list of optical mapping related file formats:
OMTools
ref – data file
data – data file
sdata – data file
fa01 – data file
oma – alignment file
omd – alignment file
si – segment file
kc – clustering file
cbl – multiple alignment file
cbo – multiple alignment file
cbc – multiple alignment file
All OMTools file format can be found in
https://github.com/TF-Chan-Lab/OMTools/blob/master/OpticalMapFileSpecification.pdf
OMSV
osv – structural variation file
Bionano Genomics Inc.
bnx – data file
The raw data file generated by Bionano Irys / Saphyr system. It contains extra information such as signal intensity and signal-to-noise ratio.
https://bionanogenomics.com/wp-content/uploads/2018/04/30038-BNX-File-Format-Specification-Sheet.pdf
cmap – data file
The data file used to store reference or assembly. It contains extra information such as label quality and signal coverage.
xmap – alignment file
The default alignment output by RefAligner.
smap – structural variation file
The structural variation output.
align – alignment file
An intermediate pair-wise alignment file.
spots – data file
An old data file format.
OpGen Inc.
xml – data file
The data file used by OpGen Inc.
Maligner
maps – data file
aln – alignment file
The page explains the input and output of maligner.
https://github.com/LeeMendelowitz/maligner/wiki/Input-and-Output-Files
SOMA
opt – data file
silico – data file
TWIN
psl – alignment file