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Old 02-12-2010, 06:40 AM   #1
Mona
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Default Velvet Parameters

hi,
i m working with the de-novo assembly of bacterial genome, that has been sequenced using Roche 454. I m trying to assemble the sequnces using Velvet assembler and viewing the assembly with Tablet viewer. On viewing the assembly performed by Velvet in tablet, i get very high percentage of mismatches like 60% to 90%. i think, i m not setting the parameters like kmer length, expected coverage and coverage cut off appropriately. Can anybody please tell me what are the appropriate values for these parameters and also i cant fully understand these terms. so can anyone please make these things clear to me.
thnx
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Old 02-12-2010, 08:05 AM   #2
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Default velvet

You can try with plotting in R, look the velvet manual (choice of coverege cutoof).
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Old 02-12-2010, 10:11 AM   #3
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yes i have read that but still could not understand that. need some easy description of these things. as i m ver much new
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Old 02-12-2010, 10:43 AM   #4
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ya the only way is u have to test run with small data set by using different parameters and alos try to check these assemblies by using a denovo assembly viewer and then you can get an idea regarding the parameters..
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Old 02-12-2010, 11:06 AM   #5
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Velvet does not assemble 454 reads very well - you should really try Newbler
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Old 02-15-2010, 12:50 AM   #6
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ok thnx all!
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