Entering edit mode
3.9 years ago
shelkmike
★
1.2k
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:
- You provide it with a starter. It can be a contig from some other assembly or just a random read.
- It maps reads to the 3' end of the starter.
- It calculates a consensus of reads that overhang the 3' end and extends the starter.
- 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
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)
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.
good point indeed. thx
What will be the behavior on a circular genome? Will it stop when 5’ end and 3’end overlap?
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.
Is there any de-novo Mitochondrial genome assembler which can accept long reads (Nanopore sequence)?
As far as I know, no. You can use whole-genome assemblers, like Canu and Flye, and then search for mitochondrial sequences among their contigs. Alternatively, you can take a gfa file produced by such assemblers and give it to GetOrganelle. See the part that starts with "To extract the plastid genome from an existing assembly graph..." at https://github.com/Kinggerm/GetOrganelle , this works with mitochondrial genomes as well.