This is a test version of Biostars. For the public version, visit https://www.biostars.org.
reference-guided assembly tools for short read data?

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!

genomics assembly
• 2,151 views • link
updated by Ram Ram • written by Hani • Hani

2 answers

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)

• 0 views • link
written by lieven.sterck lieven.sterck

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

• 0 views • link
written by Hani • Hani

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

• 0 views • link
written by Hani • Hani

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

• 0 views • link
written by michael.ante michael.ante

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:

• 0 views • link
written by lieven.sterck lieven.sterck

The CLC Genomics Workbench can help you, below is a video tutorial showing you the process.

Also, here is a paper where they used the CLC Genomics Workbench for whole genome sequence bases synteny analysis: https://www.nature.com/articles/s42003-024-06738-w

Video tutorial: https://tv.qiagenbioinformatics.com/video/113782642/de-novo-assembly-blast-and-genome-2

De novo assembly, BLAST and genome finishing using CLC Genomics Workbench

This webinar will introduce users to the tools available for short reads (Illumina) as well as long reads (Oxford Nanopore, Pac Bio) de novo assembly in CLC Genomics Workbench. It will also go over other useful functionalities such as BLAST and genome finishing.

Participants will learn the following:

o Download and install needed plugins.

o Import data required for the analysis.

o Run the de novo assembly workflow.

o For long reads, improve a de novo assembly by polishing with short, high-quality reads.

o Map reads to a reference and visualize an assembly.

o For long reads, correct raw long reads for further analysis.

o Use BLAST to investigate the contigs.

o Analyze and assemble contigs through Genome Finishing tools. Related videos

Two week free trials are available on the Genomics Workbench webpage and technical support is provided during that period if needed.

Good luck!

• 0 views • link
written by Nicole • Nicole

Log in to answer this question.

More posts like this