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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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Lowering the minimum size for sinteny blocks #48

Closed salvocamiolo closed 5 years ago

salvocamiolo commented 5 years ago

Dear Authors,

I used Ragout on some viral genome and the analysis was very successful. However I can not use Ragout on all the viruses I usually work with because the minimum sequence size to be considered in the synteny blocks is 5000 bp. Several viruses feature a genomic size of less than 10,000 bp and somtimes segments of 1000 bp or less. Do you think that you may release a version of the software that can handle such short genomes. That would be interesting to test to see whether the promising results I obtained so for on bigger viruses can confirmed on smaller ones. Thanks a lot for you support

mikolmogorov commented 5 years ago

Hi,

Thanks for the feedback!

Sure, you can use custom synteny block size as described here: https://github.com/fenderglass/Ragout/blob/master/docs/USAGE.md#synteny-block-scale

salvocamiolo commented 5 years ago

Hi Mickhail,

thanks for your message. Sorry about that, I actually hadn't seen this part of the manual. Everything was sorted out according to your suggestion best regards Salvo

Il 10 lug 2019, 02:46 +0200, Mikhail Kolmogorov notifications@github.com, ha scritto:

Hi, Thanks for the feedback! Sure, you can use custom synteny block size as described here: https://github.com/fenderglass/Ragout/blob/master/docs/USAGE.md#synteny-block-scale — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.