Problem with Newbler 2.6 with 454+Illumina data

[markestine]

Hi,

I try to use Newbler 2.6 to reconstruct eucaryote transcriptome from 454 + Illumina SE data (100pb).
I made few test but it’s very long : 1 week for 500.000 reads 454 + 85 millions reads Illumina.

I run this command line :
/runAssembly -cdna -cpu 8 -mi 95 -ml 40 -urt fastq_file sff_file.

I have many problems :
1) Newbler recognize my fastq_file as a pairend fastq, while it is not the case. Anybody have a explanation?
2) Why the job is so long?
3) The parameter -ml 40 is it rigth? or I should try a other values?

Thank in advance,

[Seqasaurus]

ml 40 is fine. 1 week isn't long considering you are using 85 million illumina reads! In the past I used 1.2 million gs flx reads and 2 millions 100bp se hiseq2000 reads for a eukaryote transcriptome. This completed in about 2 days on a desktop with a quad core i5 processor and 16gb of ram under newbler2.6. Do you really need to use all 85 million illumina reads? I suspect not

In an earlier version of newbler i noticed a delay when trying to assemble data in different formats i.e. fasta+qual and sff was slower than assembly everything in fasta+qual format.

Never used urt option so don't know if this increases time required

[gridbird]

try "-large" parameter for higher abundance data. It may speed up.

Hi,

I try to use Newbler 2.6 to reconstruct eucaryote transcriptome from 454 + Illumina SE data (100pb).
I made few test but it’s very long : 1 week for 500.000 reads 454 + 85 millions reads Illumina.

I run this command line :
/runAssembly -cdna -cpu 8 -mi 95 -ml 40 -urt fastq_file sff_file.

I have many problems :
1) Newbler recognize my fastq_file as a pairend fastq, while it is not the case. Anybody have a explanation?
2) Why the job is so long?
3) The parameter -ml 40 is it rigth? or I should try a other values?

Thank in advance,

[RCJK]

I think "-large" is not recommended (maybe not allowed?) for cDNA assemblies.