Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Reference Genome?

Question

[Tianyang Li]

Hi

Are there existing tools for visualizing RNA-Seq splicing graphs from de novo assembly without a reference genome?

What I'd like is something that can show how read goes from one exon to another and the coverage of each exon.

Are there such tools using only contigs assembled by a de novo assembler and the reads?

Thanks!

Answer 1

[Pascal]

Hi,

take a look at "CBrowse". It is made for de novo assemblies and works with SAM/BAM files. I haven't used it myself, but I think this is what you want.

Here is the link to the publication: http://bioinformatics.oxfordjournals.org/content/early/2012/07/12/bioinformatics.bts443.abstract

And their web site: http://www.conifergdb.org/CBrowse

[Farbod]

is this link correct ?

[GenoMax]

This appears to be the new home of CBrowse.

[Tianyang Li]

I've looked at this paper but it seems it's too complicated to set up and its functionality is a bit lacking.

Answer 2

[guillaume.gautreau44]

I suggest : Bandage https://rrwick.github.io/Bandage/