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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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tigmint-make: minimap2 is being called with -y argument #72

Closed mmokrejs closed 2 years ago

mmokrejs commented 2 years ago

Hi, I wonder what the -y argument does. It is not documented in minimap2 --help. Should that be -Y instead?

-Y use soft clipping for supplementary alignments

I refer to line https://github.com/bcgsc/tigmint/blob/master/bin/tigmint-make#L225

lcoombe commented 2 years ago

Hi @mmokrejs,

Here's the description of the -y option from the full minimap2 manual page (man minimap2):

       -y        Copy input FASTA/Q comments to output.

That option is needed to retain the pseudo-linked read barcoding information in the output alignments.

mmokrejs commented 2 years ago

Aah, thanks, did not think the help output is incomplete.

lcoombe commented 2 years ago

No worries! Yes, some of those less-common options can be less obvious to find!