Complete of Illumina raw reads

Question

[A_heath]

Hi all,

I have at my disposal raw paired-reads from Illumina sequencing and I would like to assemble them. The ideal goal would be to have a single contig for this assembly. This is my first real assembly so I would like to have some advices, please.

In order to assemble these reads, I am using SPAdes for the assembly, and then circlator to circularize the genome.

Do I need additional softwares to improve my assembly? For instance, error correction tools like BFC https://github.com/lh3/bfc ?

Thank you for your much appreciated help!

Audrey

[andres.firrincieli]

Do I need additional softwares to improve my assembly? For instance, error correction tools like BFC https://github.com/lh3/bfc ?

keep in mind that spades has is own error correction step if you include the option --careful in command line

Answer 1

[colindaven]

Unicycler https://github.com/rrwick/Unicycler is great software which seems to be able to use Illumina only reads, even if best results are obtained using long reads corrected with Illumina.

I've never seen a bacterial genome as one contig following Illumina only assembly.

[A_heath]

Thank you so much for your reply. I'm trying to use Unicycler but I can't install a dependency called "pilon". I looked online but I'm still unsucessful. Do you have a way to install it so that it works for Unicycler?

edit: I found a solution and was able to install pilon! Thanks again for the help.

[colindaven]

Please set up bioconda properly if it works in your environment/workstation/cluster

You can then install pilon (and unicycler, I believe) from bioconda.

https://bioconda.github.io/recipes/pilon/README.html