[mira_talk] Re: mira an assembly combiner?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 8 May 2013 17:25:04 +0200
On May 7, 2013, at 8:35 , Steven Robbens <steven.robbens@xxxxxxxxx> wrote:
> My question: can I use mira to perform this second round of assembly, based
> on an existing assembly rather than using individual reads? Can this be seen
> as a kind of hybrid assembly? Or should I use tools like CAP3?
Hrm. Difficult question to answer as I do not know what your "target" was. A
gene sized fragment? A BAC, YAC or genome?
Should your target contain consensus reads >=20kb, you will need either to
fragment them or use other tools. If you work with MIRA, give every target its
own strain, make the technology "text" and (maybe) use some of the clustering
parameters
like for EST clustering.
Please read
http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html#sect1_est_difference_assembly_clustering
and
http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html#sect2_using_mira_for_est_clustering
Hope this helps,
B.
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