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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