Tool: Elloreas, a new genome assembler
gravatar for shelkmike
8 months ago by
Russian Federation
shelkmike370 wrote:

Hi everyone

I've created a new genome assembler named Elloreas (an abbreviation for ELongating LOng REad ASsembler). Simply speaking, it works in the following way:
1) You provide it with a starter. It can be a contig from some other assembly or just a random read.
2) It maps reads to the 3' end of the starter.
3) It calculates a consensus of reads that overhang the 3' end and extends the starter.
4) It goes to the step "2)".

There are many similar assemblers for short reads, like TASR, Mapsembler2, NovoPlasty and others. However, as far as I know, Elloreas is the first such assembler designed for long reads from PacBio and Nanopore.
A useful feature of Elloreas is that if it sees several alternative extensions for the contig, it will tell the user about their existence and give their sequences too.
You can read more about Elloreas here:

tool next-gen assembly • 409 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by shelkmike370


Do you know of the MASURCA assembler? it uses a similar approach (initially for short reads , but nowadays also for long(er) ones I think, not sure though)

ADD REPLYlink written 8 months ago by lieven.sterck10k

Yes, I know MASURCA. MASURCA is very different from Elloreas. For example, MASURCA is a de novo assembler, while Elloreas was designed first and foremost for local assembly.

ADD REPLYlink written 8 months ago by shelkmike370

good point indeed. thx

ADD REPLYlink written 8 months ago by lieven.sterck10k

What will be the behavior on a circular genome? Will it stop when 5’ end and 3’end overlap?

ADD REPLYlink written 8 months ago by Juke345.2k

After every iteration Elloreas checks whether there is a long overlap between the 5' and the 3' ends. If such an overlap exists and has a sequence similarity of 100%, then Elloreas stops and tells the user that the genome has probably circularized.

ADD REPLYlink written 8 months ago by shelkmike370
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1563 users visited in the last hour