This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to remove contamination from NGS data

Hello,

I got 2 DNA samples from bacteria of the same species sequenced using Illumina platform. Unluckily, one sample was contaminated with bacteria from the different genus bacillus. There is a clearly different peak in GC content. How can I remove the sequences which are due to contamination?

I tried to identify the contaminating seuqences by aligning my sample contigs with Bacillus contigs from database using the Mauve software. I can clearly identify large parts of the contamination but there are unaligned contigs in the end of each sequence which I do not know where they belong to. Here is the Mauve screenshot. Dark green regions are the target sequences.Light green the contamination from Bacillus. I dont know what to do with the red parts. http://s20.postimg.org/5jre11ubf/bacillus_2_3.jpg

Does anyone know how to solve the problem without sequencing again and loosing as little information as possible?

Thanks a lot.

next-gen
• 5,342 views • link
updated by Mo Mo • written by olp123 • olp123

3 answers

Use BBsplit from BBMap. Provide the two (or one correct) genomes to bin the reads. You may lose some reads that will not map uniquely but that can't be helped. You could choose include them in both bins.

• 0 views • link
written by GenoMax GenoMax

I can recommend BBSplit: a description can be found here.

[Edit] Ninja'ed by GenoMax!

• 0 views • link
written by harold.smith.tarheel harold.smith.tarheel

have a look at this package in R, it showed promising results http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843372/

• 0 views • link
written by Mo Mo

Log in to answer this question.

More posts like this