Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads

Question

[WCG3]

Hello,

I'm trying to do a de novo assembly of a mycobacterial isolate that is likely similar to one of several published complete genomes on NCBI that I am hoping to use as a reference. I was able to use SPAdes to assemble contigs from Illumina PE reads, but now I have a few thousand contigs that need to be arranged. Anyone have suggestions for (preferably Galaxy or open source) tools to align contigs to a published similar species reference? I wish I had some long reads, but alas, I do not.

Thanks!

Wayne

Answer 1

[Tm]

You can use nucmer program of MUMmer package for aligning your denovo assembly to reference genome and can upload its output file (.delta) to assemblytics. It will give you interactive dot plot (by arranging denovo assembled scaffolds on reference genome) as well as helps in analyzing variants between two genomes aligned.

[robert.murphy]

That would not be a reference guided assembly though would it? this would just allow for comparison of a reference to a de novo assembly?

Answer 2

[colindaven]

Medusa may work https://github.com/combogenomics/medusa

Answer 3

[jean.elbers]

Ragout (https://github.com/fenderglass/Ragout) is also another option.