After analysing the NGS data ( Illumina reads), I have got a contaminant bacteria (marine Bacteria) along with my target bacteria ( Cyanobacteria). The total size of the genome is 14 MB. The annotation result shows two copies of 16s rDNA and two copies of 23s rDNA are present. One is for my target organism and another one is a marine bacteria. How to remove the contaminant bacteria from my target genome?
1. Since your samples sounds metagenomics samples, I would not call the final assemblies genomes. I guess it would be better to call them MAGs.
2. The size of assembly is too big to be a (Cyano) bacterial genome. The larget cyanobacterial is no more than ~9Mb long. So, if your assembly is 14 MB, surely is has way too much contamination.
3. "How to remove contamination" - it largely depends how you process your data. It is highly specific question which simply can not be generalized based on the provided information.
Abhijeet Singh Thank You very much for your response. I just want to extract my Target genome sequences (Cyanobacteria) from the 14 MB assembly.
Hi!
I would recommend you to have a look at these links:
" How can I remove contaminants from an assembled genome? (biostars.org/p/480949/) "
(13) What methods/programs are recommended to clean-up a genome from contaminating reads? (researchgate.net/post/What_methods_programs_are_recommended_to_clean-up_a_genome_from_contaminating_reads)
(13) (PDF) Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets (researchgate.net/publication/50400048_Fast_Identification_and_Removal_of_Sequence_Contamination_from_Genomic_and_Metagenomic_Datasets)
I hope it helps,
Best regards
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