[mira_talk] Metagenomic 454 Titanium Assembly
- From: Ryan Lesniewski <lesn0011@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 13 Jan 2010 17:16:02 -0500
Hello,
First, I want to say that MIRA is an incredibly flexible, and
well-documented/explained program....big thanks! It is incredibly hard to
come by this rare breed these days.
Now, my big question is: Is MIRA flexible enough to handle about 2 million
(~350 bp avg.) metagenomic reads from an environmental sample? Of course,
this dataset has many different organisms. Can I strap up the quality and
stringency so that I can get organism specific, non-chimeric contigs? Do
you have recommendations for parameter adjustments?
I have been playing around with the program and I have been successful in
getting many large contigs, but I am in the process of visualizing the read
assembly.
I also have metatranscript(cDNA) datasets from the same environments. Any
suggestions on using the EST function to assemble some of the transcripts?
Any feedback is greatly appreciated.
Cheers
Ryan
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