Moleculo for non-human?

[cement_head]

Hello,

Has anyone tried, or know of anyone, using Illumina's Moleculo Kit on non-human genomes? Or is it really only for use on human?

Regards,
Andor

[GW_OK]

Illumina themselves have done C.elegans genomes with it, so I suppose it's good to go for non-humans.

[GenoMax]

Rice genome also mentioned in this tech note: http://res.illumina.com/documents/pr...t-assembly.pdf

[nucacidhunter]

Illumina has 6 data set which are downloadable from BaseSpace. One is for human phasing and 5 are for long read assembly inclding two mentioned above. Phasing is offered only for human which I gusse it is because of limitation in bioinformatics. Library prep workflow is similar with a few differences between two applications.

[westerman]

I keep trying to get one of our customers to try it out but it seems like everyone is focused on 'cost per base' instead of 'value per base'. :-(

[nucacidhunter]

PacBio is cheaper and better option for long-read applications. Illumina's method suffers from PCR bias and is less succesful in assembling long reads from repeatative regions evidenced by very low repeat content of output in comparison to input genome.

[westerman]

@nucacidhunter:

Any backup for that statement? Not that I have reason to doubt you -- I really do not know -- but if we are going to advise our customers to use PacBio or moleculo then it is good to have a solid reference.

[GenoMax]

Is BaseSpace a requirement to analyze data from these kits?

[nucacidhunter]

I have not seen any published work. But you can download current data from BaseSpace and check for percentage and length of retroelements and transposons in long reads and compare it to reference genomes.

[nucacidhunter]

The run has to be set up for uploading into BaseSpace and there is one app for long read assembly and another one for phasing experiments. Cost of BaseSpace use included in library prep kit so there is no charge for analysis.

[GenoMax]

That would not work for many institutions. Local security considerations prevent use of cloud computing (certainly for human data).

[cliffbeall]

Just thought I would add that there is this preprint on Drosophila:

http://biorxiv.org/content/biorxiv/early/2014/01/19/001834.full.pdf

[cement_head]

PacBio is cheaper and better option for long-read applications. Illumina's method suffers from PCR bias and is less succesful in assembling long reads from repeatative regions evidenced by very low repeat content of output in comparison to input genome.

PacBio's quality is atrocious - maybe worse than Ion Torrent

[cement_head]

That would not work for many institutions. Local security considerations prevent use of cloud computing (certainly for human data).

but...as long as the data is anonymised its just a fastq file...

[GenoMax]

PacBio's quality is atrocious - maybe worse than Ion Torrent

This publication begs to differ: http://www.biomedcentral.com/1471-2164/15/699/abstract. So would I. With the right (and good quality library) the results from PacBio can be very good.