Hi Sara, plz mention the type of strain is't bacterial or viral. When u working with RNA sequences, sequence coverage will be 50x to 100x. For human genome mutations or SNP study it requires 10x to 30x depth of coverage. It also depends upon application. So, let me the aim of your project. I will help u.

Hi Mahadev!

Thanks for your answer. I am working on pathogenic E. coli. Does low coverage mean, I had contamination in my strain?

No, loo coverage may result from various reasons, and contamination is not the first one.

Yes, it may possible. In NGS, sequence coverage describes the average number of reads that align to known reference bases. If any contamination observed in bacterial strains or sequence of such strains doesn't align to known reference bases with certain degree of confidence. You can check the vector sequence contamination with the help of Vecscreen software tool which is available on NCBI.

Based on experience, this kind of issue may effect you number of contig mean produce high no of contig, the probability of contamination also high. 30X usually use for re sequencing approach and not for denovo it should 50X above (standard NGS is 100X). Recommendation is to identity the yeaid whether it final output. 2. identify the read is belong too which organism (homology method of you contig or you may use kraken to classified you read).