How to separate sequences of two species from Metagenomics Analysis?

Question

[hafiz.talhamalik]

I have sequenced a genomics data. This contains ecoli and naegleria fowleri, and I want to separate both of them so I could assemble naegleria fowleri genome. Any Idea how to separate them from fastq files??

[Joe]

You could try profiling with kraken/centrifuge. I believe they will separate out the reads for you too (I could be wrong).

[hafiz.talhamalik]

OK I will try that and will let you know.

[Nitin Narwade]

In this case you can use fastqscreen or bbbbsplit.sh (module available under BBMap package.

Both the tools will map your raw reads on multiple reference genomes.

NOTE: In this case you have to consider unaligned reads (failed to map on any of your reference genomes) for assembly construction.

[hafiz.talhamalik]

oh great.! I think these will serve the purpose.

[Nitin Narwade]

Dear hafiz.talhamalik,

If my suggestion somehow helps you to get an idea for resolving your query, could you please hit on upvote button?

Thank you.

[shenwei356]

Try mapping to E.coli first, check the coverage (they may share some genes), and assemble with unmapped reads. It may be hard to separate If they share some genes.