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
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.
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.
Please set up bioconda properly if it works in your environment/workstation/cluster
You can then install pilon (and unicycler, I believe) from bioconda.
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keep in mind that spades has is own error correction step if you include the option
--carefulin command line