Binned input for Megan

Question

[ARich]

Dear Biostar users,

I have very basic question regarding megan input. I would like classify my binned reads using megan. The question is can i use these binned reads for blastx against nt database or blasting contigs against NT database in only appropriate?

Thank you in advance!

[gb]

I think we need more info. I assume that you want to know which species are present in your sample. Maybe using metaphlan can help http://huttenhower.sph.harvard.edu/metaphlan2. Also think about the classifying part, just blasting all the reads and classifying them is a bit useless due to things like household genes and other parts of the DNA that are not distinctive for a certain species. MEGAN will say that the read belongs to a certain species but your top 50 blast hit are all a 100% match all with different species. Maybe after binning you can somehow vind marker sequences like 16S, 18S, CO1, ITS depending on your sample and blast those and then use megan if necessary. Megan is only useful if you don't have a significant good blast hit to check the lowest common ancestor.

[GenoMax]

Can you clarify what "binned reads" means here?

[ARich]

Means reads which are assembled with Spades are then binned based on compositional and taxonomic similarity using CONCOCT,Maxbin etc

Answer 1

[colindaven]

I think your

Start - normal fastq reads

Assembly with SPADES - Contigs

Neither of these are binned reads. Contigs are essentially contiguously assembled groups of reads.

Maybe you want to restart and try using eg Diamond or similar to compare the initial read set to a database ? Then you can read the results into a tool like MEGAN for analysis.