Groom data prior to using GS de novo Assembler?

[grassgirl]

Hello forum members,

I'm running GS de novo Assembler on 454 junior data and I'm wondering if folks groom the data based on qual scores before running the assembler. I can pass in the sff file, which contains the qual data, so I assume the assembler does something with the qual data. The qual scores on isotigs from a recent run were very good and I have also read from others that using the sff file produced a better assembly than simply passing the read file without the quals. I tried to get an answer from the manual (as far as qual cutoff for reads), but found none.

Any ideas?

[flxlex]

I never 'groom' as newbler (gsAssembler) is doing this for me :-) Using the quality data from the sff file, as you wrote...

[grassgirl]

Hi flxlex,

Thanks for your reply. Do you know what criteria newbler uses (e.g., a lower cutoff of qual 10 or something)?

[flxlex]

Sorry, no clue...

[grassgirl]

Well, I will try and find an answer and if I do I'll post it here.

Thanks.

[grassgirl]

I contacted Roche and this is what the rep told me:

"The quality scores are not used to eliminate reads from the GS Assembler - the only input reads that are eliminated are those that are 'Too Short' (less than 50 bases)

During the assembly, it will generate consensus basecalls of the contigs by using quality and flow signal information for each nucleotide flow included in the contigs' multiple alignments.

If you were to just give it the fasta file and no quality scores it would make the assumption that the quality is good.

You can change the stringency of the quality filters during signal processing if you wanted to eliminate reads."

The second paragraph is from the manual. Still a bit of a black box, but I'm guessing that a particular base is called from the highest qual-scoring read(s) and the consensus drawn from that, then the qual score for the isotig/contig is given.

I guess the thing to do is filter your isotigs/contigs based on qual scores prior to further processing. Have you done this before Blasting flxlex?