Hybrid Assembly approaches and advantage of having a circular genome assembly
0
0
Entering edit mode
15 months ago
SergeW ▴ 10

Hi all,

I'm currently busy trying out different short, long and hybrid (Illumina+Nanopore) assemblers on real and simulated bacterial data (isolates). I've been focusing on Unicycler, HASLR and HybridSPAdes for the hybrid assemblies and Canu, Flye and Unicycler (Miniasm) for the longread-only assemblies.

My first question is; what is the main difference/advantage in using Unicycler vs a longread assembler (ex. Flye) + Pilon polishing approach? It seems like Unicycler is heavily dependent on the short read assembly it performs.

My second question is; what's the advantage of having a circular genome assembly (for example using Circlator) when your assembly is linear but accurate and complete overall (especially the ends).

Thanks in advance! Any tips and advices on assemblies/polishing/pre-processing are welcome.

Kind regards,

Serge

Assembly genome • 467 views
ADD COMMENT
0
Entering edit mode

Hi, were you able to find the answer?

ADD REPLY

Login before adding your answer.

Traffic: 1789 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