Assembler for only nanopore data
4
1
Entering edit mode
3.2 years ago
ringourquia ▴ 20

Hi Everyone! Does anyone know about an assembler where the input is ONLY nanopore data (i.e, no Illumina or any other kind of short reads)? What about using ABySS for assembling only nanopore reads, is it OK? (I know that SPAdes should not be used if I have only nanopore reads)

Thanks a lot!

genomics Assembly ONT Abyss • 2.1k views
ADD COMMENT
1
Entering edit mode

Have a look here you will probably find what you want.

ADD REPLY
3
Entering edit mode
3.2 years ago
Dave Carlson ▴ 660

I believe Canu is a popular option. Should work for either nanopore or PacBio long read data.

ADD COMMENT
0
Entering edit mode

Thanks a lot Dave! I will check it out

ADD REPLY
2
Entering edit mode
3.2 years ago
harish ▴ 410

You can try Canu, Flye, Necat, Minimap-miniasm, Ra etc.

ADD COMMENT
1
Entering edit mode
6 days ago
Alex ▴ 10

Flye is working very well for us working on metagenomic nanopore data. Especially, because it offers the --meta parameter with the possibilty to assemble contig of different depth.

ADD COMMENT
0
Entering edit mode
5 hours ago
colindaven ★ 3.9k

Shasta is very good and fast, provided you have lots of RAM (over 500 GB for many genomes).

ADD COMMENT

Login before adding your answer.

Traffic: 2058 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6