Velvet Assembler Usage Options For 454 Sequences

Question

[Ranjit]

I have only 454 reads (300~400b) and three paired end 454 library of insert size 3kb,8kb and 20kb. Trying to assemble a genome of expected size 50-100MB. My question is - how should I specify three separate longpaired libray in velvet. Should I just consider them as three shortpaired libraries or may be combination of shortpaired and longpaired ? Any suggestions are welcome.

Thanks, Ranjit

[Ranjit]

I already tried generating assembly using Newbler but was looking if other open source programs performs better. What other programs are suggested in this case apart from Newbler? Thanks.

[SES]

AllPaths and the Celera assembler are appropriate for long reads. There is a new variant of Celera called MSR-CA, but I can't offer any experience with it. AllPaths should work good if you have long and short insert libraries, but Newbler should give you a good result for that genome size.

Answer 1

[SES]

I would not use Velvet for this data set; Newbler or AllPaths are more appropriate and will likely give you a better result. Is there a reason you are not using Newbler (Roche's gsAssembler)?

[Yannick Wurm]

yes, just use Newbler.

[Ranjit]

Thanks for the answer. I already tried generating assembly using Newbler but was looking if other open source programs generate better assembly. What programs you suggest in this case apart from Newbler?