Determining a complete genome from contigs

Question

[Optimist]

Hello all,

How to determine the complete genome from a set of 192 contigs. Which are the tools to be employed to acheive this?

I have a genome fasta file with 192 contigs.

thanks a lot

[Puli Chandramouli Reddy]

Hi, The question is bit unclear. If you want to know whether these contigs cover complete genome or how much percentage is covered, you can use BUSCO

[Optimist]

Hello Puli Chandramouli Reddy, I had downloaded a Bacterial genome from NCBI for genomic analysis. I has 192 contigs in it. So, if I have to map the various virulence factors and Resistance genes that are present in the genome, I need a complete genome without any missing sequences. So in order to get a complete genome Is it fine if I reorder the 192 contigs using MUMMER and concatenate them to get the complete geneome. Am I following the right protocol to get a complete genome or are there any other methods to get the complete genome.

[Puli Chandramouli Reddy]

What is your reference genome? you will get an idea about percentage of aligned contigs to reference genome using MUMMER and thus the coverage. Why cant you align target genes directly on these 192 contigs and get idea about it?.

[Optimist]

Hello Sir,

My reference Genome is Pseudomonas aeruginosa PAO1. How do I contact you sir? I need to discuss the issue and get things clarified directly from you.

Thanking you Sir

[Puli Chandramouli Reddy]

Please do not call me Sir.

You can discuss in this forum and you may get better suggestions than mine as many experts will read your queries.

Answer 1

[ropolocan]

Mauve can also be an option for this.