Tool: Elloreas, a new genome assembler
2
gravatar for shelkmike
5 months ago by
shelkmike290
Russian Federation
shelkmike290 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: https://github.com/shelkmike/Elloreas

tool next-gen assembly • 344 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by shelkmike290

interesting.

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 5 months ago by lieven.sterck9.1k
1

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 5 months ago by shelkmike290

good point indeed. thx

ADD REPLYlink written 5 months ago by lieven.sterck9.1k

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

ADD REPLYlink written 5 months ago by Juke344.9k
1

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 5 months ago by shelkmike290
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