reference-guided assembly tools for short read data?

Question

[Hani]

Hi, maybe a silly question. I have a bunch of short read data for ~20 accessions of a plant species. I also have a pretty high quality reference genome. I've been working with the short reads to do variant calling, and was wondering if I could possibly make a sort of draft assembly for each accession? Mapping my read pairs to the reference produced ~98% reads mapped so I know that everything is pretty closely related to my reference.

I was interested to see if I could generate a .fasta to do stuff like synteny analysis and the sort. Has anyone done something like this before? Is this a silly thing to try? I am pretty new to this field so I am unsure.

Thank you to anyone!

Answer 1

[lieven.sterck]

Not silly at all and done before many times. So yes that is a valid approach. There are certainly a number of tools around that can do this.

concerning your sentence "to do stuff like synteny analysis" I'm less positive. When you do your proposed approach you will mimic what is in the reference so any synteny analysis becomes a bit obsolete (== in that sort of analyses you are looking for difference/similarities between genomes given that they are independent assemblies ). If you do a denovo assembly of each of your accessions you do have valid synteny analysis data input (but will require most likely different tools than the reference-based approach)

[Hani]

In regards to your comment about synteny analysis, I suspected that would be the case. In regards to tools for these purposes, do you personally have any recommendations?

Thank you for your time by the way

[lieven.sterck]

which purpose specifically?

[Hani]

Either de novo or reference based genome assembly using Illumina PE short reads

[michael.ante]

I don't know how well it works for plants, but I worked with Saute and it was doing well for reference based assemblies.

[lieven.sterck]

there are several options to choose from, doing a quick google search will give you a lot. The main thing to keep in mind is to choose one that is suitable for plant species (most of them are suitable for several different kind of species but some are somewhat tailored towards specific genera/kingdoms )

alternatively to googling you can search lists that are available online:

• https://en.wikipedia.org/wiki/List_of_bioinformatics_software
• https://github.com/RipollJ/awesome-bioinfo-tools
• ....