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. 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.