[mira_talk] Re: Assembly of NCBI Data
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 9 Jan 2011 01:05:07 +0100
On Freitag 07 Januar 2011 Thomas, Dallas wrote:
> Have 13,900 sequences comprised of NCBI nt, est and gss data. This is
> just the fast information obtained from NCBI. Looking at doing a
> de-novo assembly on the data, however am a bit baffled on the --joblist
> and options I should be using. Does one just use sanger? Or would one
> assume that a high proportion of est, etc might come from 454? Would
> you use "est" in the joblist for all of the sequences or assembly only
> the est using "est" and use genome for the gss and nt.
If in doubt, try
--job=est,denovo,draft,sanger
and see how it behaves (the assembly) and how the results look like. If far
too many contigs get made due to differences which look like homopolymer
errors, try 454.
B.
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