Re: [Broad Viral Tool Users] Vicuna Contigs

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Xiao Yang

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Apr 11, 2014, 9:10:16 AM4/11/14
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Hi, 

I try to respond to your questions below.


On Thu, Apr 10, 2014 at 11:04 AM, Bede Constantinides <bed...@gmail.com> wrote:
Hi there,
I am trying to benchmark Vicuna for HIV and HCV assembly. However, Vicuna typically generates hundreds of contigs in real datasets. Is this to be expected?

Yes, Vicuna contigs were further merged via V-Fat program.
 
Am I correct in saying that the contig.fasta file should contain a single consensus sequence if all goes well?

Not necessary, I dont' think any assembler would guanrantee this.
 
Even when assembling simulated low error clonal HIV reads (100x reads generated by MASON with default 454 error profile, run through fakePairedReads.pl), Vicuna outputs 22 contigs. Other assemblers I have tested easily build a single contig from this dataset.

First of all, Vicuna was meant to deal w/ Illumina paired end reads, and the input has to be paired-end.
fakePairedReads.pl is meant to facilitate the assembly of 454 reads, i.e. simulate paired-end data as
if they were Illumina. In your simulated data, since the reads are fairly long and you mentioned low error
rate, I think 454 assemblers should do fairly well. 
 
I am using default settings, specifying only input and output files.

I feel I must be missing something obvious. What could I be doing wrong? Is Vicuna's performance dramatically improved by supplying paired end read data?

Vicuna doesn't deal w/ single end read data.
 
Linked below are the simulated HBX2 reads to which I've referred in case they are of any interest.


Many thanks,
Bede Constantinides

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