[mira_talk] Re: Metagenomic assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 11 May 2014 22:34:22 +0200
On 09 May 2014, at 23:21 , Chayan Roy <chayan.roy93@xxxxxxxxx> wrote:
> I am using six iontorrent data (avg read length 195bp) and four proton data
> (~178bp). for all data i have performed denovo assembly with default
> parameters. But after looking at the contig_stat_pass1.txt after the
> assembly, i rerun it with -AS:nop=1 (well i know this was a really weird
> things to do) but this was resulted in contigs of much longer size (in that
> case i might sacrifice the accuracy, is it so??)
You’re not sacrificing accuracy … you’re completely butchering it. Your “long”
contigs will have a lot of misassemblies.
> ..can any one give me any idea what should be the best possible parameters
> for a mapping assembly of a moderately complex community (no of species
> 700-780, with first 30 sp consists of >70% of the abundance)..
A mapping assembly? You should try the standard parameters.
> […]
> what i understand from the manual it just mapped the reads against the
> reference, nothing denovo in it??? (ofcourse i did not switch on "abnc", as
> by doing so in one case took more than 15 days to complete an assembly:()
“abnc” has been completely removed from recent version of MIRA, what have you
been using?
> how to obtain the read no stat and reads used in the reference based mapping
> assembly for each contig in seperate files??
Uhm … I did not get that question.
B.
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