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tanghaibao / quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)
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Working with non-model organisms #12

Closed madzafv closed 3 years ago

madzafv commented 6 years ago

Hi! I want to check for synteny between the zebra finch genome available at ensembl and a the genome of another finch, which is still unpublished and was ensembled, mapped and annotated by a collaborator using several sources. Can quota-alignment help me? Or would you recommend any other tool that could? LASTZ, Mummer, SyMAP, Satsuma, SynMap, Enredo/Pecan, HAL... Thanks!

tanghaibao commented 6 years ago

@madzayasodara Probably the easiest way is to upload your genome onto CoGe, which contains an implementation of QUOTA-ALIGN, plus some other tools including SynMap (synteny viewer) and GeVo (local synteny browser). Please feel free to contact the CoGe developers if you run into issues.

Haibao