Hi, we have sequenced 6 bacteria of same species on an NGS platform. When we aligned the data to the reference the alignment was only 2%. When we checked for a possible contamination, the sequences aligned to different bacterial SPS.
Are there any tools to check for contaminating sequences in the data we generate?
Thanks in advance,
Ramya
Hi Robert
Yes. We got large genome sizes. When we did blast it was hitting to many different bacteria. What do we infer from this?
What indexing system did you use for the run? Normally, low level contamination on illumina platforms can be solved by dual indexing alternating between consecutive runs and thourough wash with chloride - Tween solution in-between runs. For tools, you can try CheckM from GenomeBiology that was recently published.
Hi
These reads were generated on Iontorrent PGM. Any suggestions further?and it has its own indexing system as barcodes. And thanks for information on the tool. will look into it.
Thanks once again.
did you use HiQ chemistry or older one? Please, contact: Jan at Ziegler, Jan . He is indeed very helpful in addressing all questions of PGM.
Good luck!
Why are you asking this? You just did it. Everything mapping with high quality on unexpected genomes, it is a contamination. You can expect some contamination when you sequence, but 98% it seems very large to me; it makes me think that more or less all the DNA does not come from your bacteria. Depending on the size of your genome, 2% might also correspond to highly conserved genes (like 16, 23s rDNA) and therefore I would suspect that also the 2% of the reads mapping on the right genome could be a contamination (you can check this if also the 2% reads mapping on your genome also maps on other bacterial genome at the same stringency).
It depends what you expect. I usually use Kraken, which is a metagenomics aligner to align the reads to the ref seq data base of NCBI for bacteria and virus. It is straight forward and worked for me in different experiments.
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts