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mahulchak / quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
GNU General Public License v3.0
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Reg: mummer's newer version and alternatives #40

Closed harish0201 closed 5 years ago

harish0201 commented 5 years ago

Hi,

This is more of an enhancement/feature request than an issue!

Is there any reason that you are shipping mummer version 3 rather than the 4th one?

Also, given that I work with genomes > 2Gb normally, I have this query. Have you tried minimap2-> sam -> delta and then using those for quickmerge?

mahulchak commented 5 years ago

Hi Harish,

We haven't officially switched to mummer 4 yet because it is not as stable as mummer 3. However, we will keep your request in mind and will see what can be done. The mummer version included with quickmerge is 64 bit so you can easily apply it to large genomes.

You can always run mummer yourself using the mummer in your system. You can then run quickmerge on the delta file.

Mahul

On Mon, Apr 29, 2019, 22:43 Harish notifications@github.com wrote:

Hi,

This is more of an enhancement/feature request than an issue!

Is there any reason that you are shipping mummer version 3 rather than the 4th one?

Also, given that I work with genomes > 2Gb normally, I have this query. Have you tried minimap2-> sam -> delta and then using those for quickmerge?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mahulchak/quickmerge/issues/40, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZQH2GSFJI37UR6JE2MUZ3PS7L4HANCNFSM4HJIUPOQ .

mahulchak commented 5 years ago

We have not tried minimap2 -> sam->delta. We will look into that.

On Mon, Apr 29, 2019, 22:43 Harish notifications@github.com wrote:

Hi,

This is more of an enhancement/feature request than an issue!

Is there any reason that you are shipping mummer version 3 rather than the 4th one?

Also, given that I work with genomes > 2Gb normally, I have this query. Have you tried minimap2-> sam -> delta and then using those for quickmerge?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mahulchak/quickmerge/issues/40, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZQH2GSFJI37UR6JE2MUZ3PS7L4HANCNFSM4HJIUPOQ .

harish0201 commented 5 years ago

Ah, alright! Thanks for the help. Currently the biggest bottleneck is the runtime of mummer to be honest.

In the mean-time I'll check minimap2 and will correspond to you via emails if that is fine with you.

However, I'm closing the thread for the time being.