How to map contigs to the reference genome and know the start and end position?

Question

[xupbuy]

Hi experts,

I want to map my assembled contigs to the reference genome and want to know where every mapped contig starts and ends on the reference genome. And after that, I want to plot it to see where on the genome have more contigs so that I can know the enrichment region.

Is there a way to do this?

Thank you very much.

[Mehmet]

What do you mean assembled contains? Have you made a genome assembly and do you want to map your genome assembly to a reference genome? If so, you can run blast using your genome assembly as query.

[xupbuy]

Thank you very much for your reply. After I run Blast, is there a way to make a plot? like this: contig mapping to reference plot

[Mehmet]

I don't know why you want to make a plot as you said, but if you want to show a pairwise alignment between contigs and reference assembly, you can have a look mauve tool (http://darlinglab.org/mauve/user-guide/viewer.html)

[Mehmet]

I found this tutorial, which can help you.

https://taylorreiter.github.io/2017-08-10-Visualizing-NUCmer-Output/

[taylorreiter]

I have updated this tutorial, and it now lives at a different link: https://taylorreiter.github.io/2019-05-11-Visualizing-NUCmer-Output/

If you would like to see the original, the source code now lives here: https://github.com/taylorreiter/taylorreiter.github.io/blob/master/_Rmd/viz-nucmer-output.Rmd

Answer 1

[WouterDeCoster]

I think you could use minimap2 for this.

[xupbuy]

Thank you. minimap2 is like Bowtie, for reads mapping to reference. I want to map contigs to reference and make a plot like this:

[ATpoint]

These tools map given nucleotide sequences to a reference, no matter where they come from. The result will be a SAM or BAM file, which contains the respective chromosome, the start position and the length of the aligned sequence. From this, you can filter out the necessary information towards start and end.

[scchess]

The contigs are in FASTA format, and have no quality score to go into FASTQ.

[WouterDeCoster]

You don't need FASTQ or quality scores for alignment, FASTA would do just fine.