Metasim For Human Reads

Question

[matija.sosic]

Is it possible to produce human reads with metasim? If it is, which database should I use?

[ashwani.vit]

Hi,

I am trying to simulate a metagenomic dataset using metasim. Could you please let me know what does "abundance value" means.

Ashwani

[Josh Herr]

Pretty sure that is the amount you enter for read abundance, but you will want to read the paper and the manual.

Answer 1

[Josh Herr]

I'm not entirely sure what you want to do -- you weren't very clear.

I would assume you can create synthetic reads for a genome using MetaSim. I've done this for metagenomes (why it was developed), but I don't see why you couldn't do this with Human reads. Obviously you'll want to use Human database information as the basis for your synthesis. Most importantly you'll want to read the manual on how to do what you want to do.

I would consider using Heng Li's seqtk toolkit (you can use the mufta command - maybe others, see also wgsim - for this) using Human data as the basis. Best of luck.

[matija.sosic]

Thank you for your answer, What i would like to do is to simulate sequencing of microbial community consisting of human and few prokaryotes. MetaSim specifies which databases to use for prokaryotic and virus sequences, but I don't know where to find such database (or single fasta file) for human genome. That is what interests me.

[Josh Herr]

You'll want to decide which fasta sequences (or whole databases) you will need. There are many sources for human data and this question has been covered here quite often: Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File, Where To Download The Whole Human Genome In Embl Or Genbank Format With Sequences And Annotations?, and Where Can I Download All Exons Of The Human Genome In Fasta Format (One Big File!) ? are just a few.