thank for your answer.
Hi,
I tried to view with tablet AMOS file from assembly of metagenome with
meta-ray, but the file is so big (12 GB) that Tablet hangs and download is
not finish, Is this normal for big files from metagenomics?
This is head of AMOS.afg file
{RED
iid:1
eid:1
seq:
GGGCATCATCCAAGCCTATGCCATCTTCAAATGATGCGGTGGCTTAAACGCCCCACCAATAACCCTCAATGGTTTTGGTTCGGGTATTGACCCAGATAT
.
qlt:
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
.
}
Thanks
On Fri, Jun 14, 2013 at 5:18 PM, Sébastien Boisvert <
[email protected]> wrote:
> Hello,
>
>
> On 14/06/13 01:00 PM, Labo Derome wrote:
>
>> Hi,
>> To the analysis of SNPs, I need a file with the reads aligned on contigs,
>> in assembly with meta-ray, I tried with the command option " -amos"
>> but the resulting file does not seem that I need, what option can I use
>> to get a file with reads on contigs.
>>
>
> An AMOS file -- such as the one generated by Ray -- is best suited for
> visualization using high-end tools such
> as Tablet [1] or Hawkeye [2].
>
> If what you desire is a SAM file, you can align your reads on the contigs.
> I suppose there are some tools to explore
> genetic variation using a SAM file.
>
>
> Also, you can generate a kmers.txt file to visualize your metagenome graph
> with a viewer, such as Ray Cloud Browser [3].
>
>
> I know at least 3 tools that can generate these graphs: Ray, ABySS, and
> cortex.
>
> Both Ray and ABySS can dump a file that is directly compatible. You need
> to use cortex_binary_reader [4] with cortex.
>
>
>
> If you want to read more on variation mining using graphs, see these 2
> papers:
>
>
> De novo assembly and genotyping of variants using colored de Bruijn graphs
> http://www.nature.com/ng/**journal/v44/n2/full/ng.1028.**html<http://www.nature.com/ng/journal/v44/n2/full/ng.1028.html>
>
> Exploring single-sample SNP and INDEL calling with whole-genome de novo
> assembly
> http://bioinformatics.**oxfordjournals.org/content/28/**14/1838<http://bioinformatics.oxfordjournals.org/content/28/14/1838>
>
>
> ---
> [1] http://bioinf.scri.ac.uk/**tablet/ <http://bioinf.scri.ac.uk/tablet/>
> [2]
> http://sourceforge.net/apps/**mediawiki/amos/index.php?**title=Hawkeye<http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye>
> [3] http://genome.ulaval.ca:10241/**client/?map=0§ion=1&**
> region=3&location=0&depth=10<http://genome.ulaval.ca:10241/client/?map=0§ion=1®ion=3&location=0&depth=10>
> [4]
> https://github.com/noporpoise/**cortex_binary_reader<https://github.com/noporpoise/cortex_binary_reader>
>
>
>> Thanks.
>>
>
>
>
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