What Can We Do For The Reads That Are Not Mapped To The Genome?

Question

[lanyuhao1991]

I have the reads of the some mammals intestinal microflora. I mapped the reads to the bacteria genomes. And I want to use the rest of reads that are not mapped to do something. I want build some new genomes of bacterium. Can you give me some advice for: 1.how to build some new genomes of bacterium? 2.can I use the rest of the reads to do other things? Thanks!

[Buttonwood]

1.Do some assembly。 2.Map to nt/nt database for classfication.

Answer 1

[Mikael Huss]

You could use an assembler like IDBA-UD, Spades or Ray (and there are others as well of course) to do de novo assembly in order to "build new genomes" as you write. You may end up with both old and new bacterial contigs, host genome (yak) contigs and perhaps some viruses. Of course you could also try to map your unmapped reads to the host genome to remove those from the analysis, and then map the remaining reads directly to a viral reference.

Answer 2

[Haluk]

After assembling your unmapped reads, you can BLAST them to reference genome. It increases mapping rate.