Velvet Parameters

[Mona]

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

[bioenvisage]

velvet

You can try with plotting in R, look the velvet manual (choice of coverege cutoof).

[Mona]

yes i have read that but still could not understand that. need some easy description of these things. as i m ver much new

[bioenvisage]

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..

[Zigster]

Velvet does not assemble 454 reads very well - you should really try Newbler

[Mona]

ok thnx all!