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hsinnan75 / GSAlign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
MIT License
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-one option #5

Closed pjm43 closed 4 years ago

pjm43 commented 4 years ago

Hi, Can you better explain the -one option. Thank, Jeff

hsinnan75 commented 4 years ago

Hi, if the 'one' option is set, there will be no any nucleotide on query genome aligned to multiple positions on reference genome. GSAlign will only output the longer alignment and discard the short one if they overlaps.

pjm43 commented 4 years ago

Thanks for the quick response.

I did want to mention that I think the github README is wrong as it currently says to leave the defaults as is for intra-species comparisons:

Please note, if the two genome sequences are intra-species, it is recommended to run GSAlign with default parameters. However, if they are inter-species, it is recommended to run GSAlign with '-clr 50 -alen 200.'

However the current defaults are actually the recommended inter-species comparisons ('-clr 50 -alen 200') at least in v1.0.22:

image

Thanks for providing an excellent program!

hsinnan75 commented 4 years ago

Thank you! I've removed the remark.