[mira_talk] Re: Parameters not parsed

On Monday 06 April 2009 Lionel Guy wrote:
> [...]
> It was much better using the parameters in the right order (placing my  

Yep, the order is important. "--job=" sets a whole bunch of stuff trying to do 
"the right thing".

> My project:
> - sequencing a complete bacterial genome (~2Mb)
> - half a 454 Titanium run (~100Mb of data, not quite as much as
> advertised), plus 2 lanes from a titration run.
> - about 50k paired-end mates (experimental 20kb library)
>
> The bacteria that I'm sequencing experiences some kind of weird
> alternate replication in late growth-phase, leading to an (at least) 2
> fold amplification of about 10-20% of the genome, which may impair the
> uniform read distribution (I tried with urd:yes, and yielded strange
> results).

Alternate replication in late growth phase? Sheeesh ... that's some weird but 
interesting concept for a bug.

I have a new assembly engine in alpha test right now. It still has problems 
with sequencing bias in unpaired data, but it rocks when paired-end reads are 
available. The 50k PE reads might be a bit on the low end, but I'd be 
interested to know how it fares with that kind of data you have.

Please drop me a line if you're interested to run a test with the new stuff in 
development.

Regards,
  Bastien


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