Some Software That Can Assemble The Dna Sequence From Ngs Even If It Is From Mixed Microbial Sample.

Question

[always_learning]

I heard that there are some software that can assemble the DNA sequence from NGS even if it is from mixed microbial sample and present the most likely species present in that sample. Do some one have any information about that?

Thanks

Syed

Answer 1

[Mikael Huss]

At this point in time I would recommend Ray Meta or IDBA-UD, or perhaps SPAdes even though its authors explicitly state that it is not meant for metagenomics (I have found it very useful in one metagenomics project anyway.) Ray has an in-built estimation of the predicted fraction of each genome present (you need to download reference FASTA sequences from NCBI, but there is a good "Ray paper replication site" which shows how this is done). For IDBA_UD and SPAdes output, you will have to estimate the species abundance yourself, likely using some combination of BLASTin the contigs to a microbial database and mapping back your reads against the contigs.

[always_learning]

Mikael: So I am moving forward with Ray Meta, Any caveat on this from your side ? :)

[Mikael Huss]

Not really, I am happy with it, but it's possible that you need quite a bit of computing power. I am fortunate enough to have (temporary) access to an academic supercomputing cluster, so that is no issue for me right now.