Hi Zoya,

If you want to test for what is within your genomic content, construct them into contigs and BLAST the contigs  to see what the top results are.  If the sample is all your organism, then also consider the mapping parameters you are using.

I'd advise that you go back and check the parameters for your mapping.  Make sure that the distance between your paired reads is set correctly, that your reads are deduplicated, and that you are indeed mapping paired reads and not treating them as single reads.  Make sure you check every parameter you can feed to your mapping program to see if it supports the data you are using.  After mapping, use a program to visualize your mapping to see: 1) the number of paired reads that successfully paired, 2) the number of reads which did not pair (broken pairs), 3) the number of reads that did not map properly, and 4) the distance between paired reads in those that successfully paired.  Those will give you a great indication of how well your mapping went.

Good luck!

Richard W. Davis IV, Ph.D.

University of Pennsylvania

Thanks alot Mr.Ruhlemann and Dr.Davis. But i am kind of curious to know whether a very small amount of other DNA, that should not be there in my sample (lets say microalgae, eukaryotic) can affect my sequencing results?

Because i have done 16s sequencing for my samples (Pseudanabaena) and BLAST results hits 100% similarity with other Pseudanabaena sp. sequence in NCBI.

Thank you

If contaminated DNA was in your sample, the sequencing would amplify these sequences.  If there are amounts of that DNA being amplified, running BLAST on your contigs should reveal those species in the results.  De novo contig your results and BLAST them to see if you get anything other than your species.  

Hope that helps!

Thank you Dr. Davis.....For your time and efforts.

I ran into a similar problem and, as Rühlemann suggested, you should try using Kraken which I believe should be the easiest way to find out if your DNA was contaminated. Download their miniKraken database, which uses all genomes available in the NCBI database and will assign all your sequences to specific strains (viral, bacterial, or archaeal). It is pretty fast and the output is easy enough to understand. However, if that doesn't work and you suspect that eukaryotic DNA might have contaminated your samples, then running BLAST, as Dr. Davis recommended, might be your best option. 

if you have even a small amount of microalgae cell  contamination , then this will have a big effect on your sequencing due to much larger genome size of the microalgae. Which may cause it to dominate your DNA sample 

The use of Kraken is the most rapid way for checking for contaminating bacterial contamination 

Thanks everybody for answers.