Hi Ino,
Thanks for the info!
This will indeed place me in the right direction.
Cheers
David
On Tue, Jul 22, 2014 at 4:51 PM, Ino de Bruijn <ino.debru...@scilifelab.se>
wrote:
> Hi David,
>
> Quast has some nice plots that just display the assembly lengths:
> http://quast.bioinf.spbau.ru/paper/e.coli/
>
> When you map your reads back to the assembly, there are some tools to help
> you score your assembly
>
> - FRCurve https://github.com/vezzi/FRC_align
> - ALE http://www.ncbi.nlm.nih.gov/pubmed/23303509 (for metagenomics)
>
> in some cases you might want to look at the alignments themselves, in that
> case I'm quite fond of Tablet:
> - http://ics.hutton.ac.uk/tablet/
>
> Hope that helps!
>
> Cheers,
> Ino
>
>
> On Tue, Jul 22, 2014 at 11:03 AM, David Alquezar <d.e.alque...@gmail.com>
> wrote:
>
>> Dear Devoassembler users and Sébastien,
>>
>> I have recently started using Ray Meta on some Illumina (HiSeq) RNA-Seq
>> data as this tool has been used by some collaborators with great success.
>>
>> I have been trying to tweak my assemblies by varying the kmer length and
>> assessing the number of contigs, length of contigs etc. However, i was
>> curious what else can be done in this regard? Much of our work is
>> discovery, therefore, it's difficult to compare to known reference genomes.
>> Can anyone suggest other ways of tweaking the data, or visualising the
>> assemblies?
>> Thanks
>> David
>>
>>
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>
--
David E. Alquezar-Planas, PhD
Centre for GeoGenetics
Natural History Museum of Denmark
Øster Voldgade 5-7
DK-1350 Copenhagen
Denmark
Tel: +45 35321375
Mob: +45 20997831
http://geogenetics.ku.dk/
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search up to 200,000 lines of code with a free copy of Black Duck
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