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Old 02-01-2016, 03:11 PM   #1
dbob
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Default Assembling Another Genome based on a Reference

I have a bacteria sample, and I have done genome assembly and now have its original sequence. Since the bacteria sample has come from the soil, it contained two closely related bacterias. How can I use the reference genome that I now have to assemble the "other" genome? Which programs can be helpful?
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Old 02-01-2016, 04:21 PM   #2
mastal
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I think assemblers like mira and velvet give you the option of using a reference.

https://www.ebi.ac.uk/~zerbino/velve...bus_manual.pdf

http://mira-assembler.sourceforge.ne...l#chap_mapping
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Old 02-03-2016, 12:45 AM   #3
colindaven
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Try also a more recent effort, Medusa

https://github.com/combogenomics/medusa
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