Illumina de novo assembly with quality values

[Peter Bjarke Olsen]

I have been using Velvet to assemble smaller Microbial genomes using paired ends. It has worked fine but for projects with lower coverage it would be useful with an assembler that could use and generate quality values.
Does such an assembler exist? Open source or commercial.

Best regards,

Peter

[Torst]

I have been using Velvet to assemble smaller Microbial genomes using paired ends. It has worked fine but for projects with lower coverage it would be useful with an assembler that could use and generate quality values.
Does such an assembler exist? Open source or commercial.

All the traditional "Sanger" assemblers use qualities. These include Phrap, CAP3, CABOG (Celera Assembler) and Arachne. Recently these have been extended to also handle short read data - so maybe the do use the quality values.

In terms of short-read assemblers, I don't think any of them use qualities in situ - but use depth of coverage as the evidence base. You can still use the qualities for trimming reads. I agree some data sets are low coverage, but I'm not convinced using qualities would improve the assembly much. And low coverage data sets are being less common as sequencing yields increase.

[BaCh]

I have been using Velvet to assemble smaller Microbial genomes using paired ends. It has worked fine but for projects with lower coverage it would be useful with an assembler that could use and generate quality values.
Does such an assembler exist? Open source or commercial.

Peter

MIRA does. Open Source.

What's "lower coverage" for you? What are the read lengths?

B.