High throughput data from pooled genomes

Question

[k.solaymane]

Hi all, we have sequenced the whole genome of pooled organisms, we have a data set from illumina hi seq with matepair library 8kb in insert sequenced 2X100, I look for bioinformatic tool to cluster my reads within organisms etc... any suggestion ... Thank you!

Answer 1

[mikhail.shugay]

By pooled organisms you mean metagenome? You can try to start with MetAMOS (http://genomebiology.com/2013/14/1/R2), this seems to be one of the latest all-in-one frameworks in the field (please correct me if I'm wrong).

[k.solaymane]

Hi mikhail, so we have pooled our bacteria at ratio 1OD:1OD... then we performed a unique genomic DNA extraction followed by sequencing.. Thank you

[mikhail.shugay]

If you are working with known samples and have them barcoded (http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn), then you'll need to de-multiplex them. In general the instrument (e.g. Illumina MiSeq) is capable of de-multiplexing itself. Then you can proceed with each of the samples separately. Otherwise I believe that you'll have to to apply some de-novo assembling strategy that accounts for multiple organisms present.

[k.solaymane]

we haven't tagged our organisms, we have reads from the whole genomes . we want to look for % of the presence of each organism through reads..thank you for your intercation

[mikhail.shugay]

Ok then MetAMOS is the option. Good luck!