[mira_talk] Metagenomic assembly
- From: Chayan Roy <chayan.roy93@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 10 May 2014 02:51:50 +0530
Hii All,
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??)..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)..
After blast search against the few long contigs, i have selected 6
available whole genomes in single contigs, used them as a reference for a
mapping assembly which resulted in 100% length recovery although avg cov
was just 3-4..
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:()
how to obtain the read no stat and reads used in the reference based
mapping assembly for each contig in seperate files??
I know this question may be beyond the scope of this group, but any
suggestion for what kind of binning and extracting reads based on that will
improve the assembly??
thanks for any help in advance..
Regards
--
*CHAYAN ROY*
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