How to detect different chromosomes from whole genome NGS reads of a fungi?

Question

[mrj]

Hello, I have Paired-end NGS reads from a fungi. Inspecting 16S RNA points that the genome may be Aspergillus japonicus or related to it.

1. My question is how can I assemble sequence reads so that I would nearly end up with assemblies approximating to different chromosomes?

2. I was able to use SOAPDenovo2 to assemble reads into contigs. But, that does not reveal anything about the number of chromosomes. This is my very first whole genome project and I am have no idea how to achieve this.

3. Can I further assemble contigs to get at least scaffolds? If I can, could you suggest me a tool.

Thanks

Answer 1

[Brice Sarver]

1. Use an assembler suitable for your data. Saying that it is paired-end isn't enough to evaluate how the libraries were prepared or what to expect. You mentioned SOAPdenovo2, so you've presumably started to explore this.
2. You can get a sense of the number of chromosomes by looking at related species (generally, with all the caveats, e.g., ploidy changes, chromosome duplications, etc.). Have you explored the Aspergillus Genome Database or looked in the literature for karyotypes? Depending on your library prep and sequencing method, you may not have any chance of recovering chromosome-scale contigs, though you may be able to get a very rough estimate of genome size from your assembler. De novo assembly is challenging, and it is usually not a push-button analysis. Take a look at how PacBio solves assembly issues with their long reads.
3. Start with/see this paper.

[mrj]

Thank you Brice. Your answer is insightful. Thanks a lot for the paper.Indeed, I needed to hear "De novo assembly is challenging, and it is usually not a push-button analysis.".