Question: Velvet Assembler Usage Options For 454 Sequences
0
gravatar for Ranjit
8.9 years ago by
Ranjit0
Ranjit0 wrote:

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

assembly velvet • 2.3k views
ADD COMMENTlink written 8.9 years ago by Ranjit0

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.

ADD REPLYlink written 8.9 years ago by Ranjit0

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.

ADD REPLYlink written 8.9 years ago by SES8.4k
3
gravatar for SES
8.9 years ago by
SES8.4k
Vancouver, BC
SES8.4k wrote:

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)?

ADD COMMENTlink written 8.9 years ago by SES8.4k

yes, just use Newbler.

ADD REPLYlink written 8.9 years ago by Yannick Wurm2.3k

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?

ADD REPLYlink written 8.9 years ago by Ranjit0
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