Software to extend and join contigs for bacterial genome using illumina and nanopore reads

Question

[ambi1999]

Hi,

I have created a denovo hybrid assembly for bacterial genome using illumina and nonopore reads using Spades (Yes, latest version 3.13 of Spades allows hybrid assemblies using illumina and nanopore reads :) )

However the assembly is in the form of few contigs and I would like to get a complete assembly having only one contig.

Any suggestions for software that can do this specially for bacterial genomes?

I think the software should take as input the raw reads in fasta format (both illumina and nanopore reads), reference genome of closely related species.

I am currently trying to do this with AlignGraph but it only takes the illumina reads in fasta as input. So basically AlignGraph is missing out on the nanopore reads which may have added huge value in closing the gaps. Also AlignGraph seem to be giving errors related to 'BLAT CALL FAILED' which may be because of requirement to have v34 or previous versions of blat. While I am trying to get AlignGraph working, just thought to ask for suggestions for better softwares to join contig and complete the assembly.

Thanks for reading the post and any help.

Cheers,

Ambi.

Answer 1

[Leo Poorvin]

I've had good luck using Rebaler to generate an assembly from Nanopore reads and a bacterial reference genome, followed by using Pilon to polish the assembly with Illumina reads.

[ambi1999]

Thx Leo. Will try using Rebaler.

Cheers, Ambi.