How to estimate the metagenome size

Question

[ARich]

Hello Biostar,

I am doing denovo metagenomic assembly with one of the test data from literature to have hands on training.

I want to know how can I estimate the genome size?

Best,
ARich

Answer 1

[Adrian Pelin]

You can't... you are assembling a meta genome, so many genomes. Some genomes will be well covered, some not so much. My point is, the only way for you to estimate the genome size of all organisms present in your meta sample, is to look for rRNAs in your assemblies and find out exactly how many species you have, then estimate overall genome size based on other assemblies... but this does not seem informative.

[ARich]

Thank you. I Got your point. I have few more queries

1. Which assembler is appropriate out of so many or should one go with reference based assemblies(but will miss many un-annotated ones)
2. For denovo metagenome assembly how do you choose best kmers? (which statistical criteria)

Can you refer me with some tutorial for metagenome assembly (specifically for gut bacteria)

Thank you

[Adrian Pelin]

1-2)

Some DBG assemblers are said to work well with Metagenomes, for instances Ray was designed for that. Try a low k-mer, such as 41 and see what happens.

Maybe try an OLC assembler such as MIRA, these assemble without a k-mer and try to assemble whatever overlaps.

Lastly, you can try SPAdes, it allows usage of multiple k-mers in one assembly, so you can try and pick up low and high coverage.

Not sure about tutorials, try to find tutorials for the programs I suggested and start from there. All of these assemblers provide information on contig coverage, either in terms of nucleotide coverage or k-mer coverage, and that tells you something about the organism that contig belongs too.

[ARich]

Your information is really helpful because I was focusing more on Metavelvet and Meta-IDBA. Thanks a lot