I had sequenced 2 bacterial genomes using Illumina platform. The genomes were assembled and annotated which allows me to view the genetic distribution of the genomes accross my samples using SeedViewer in RAST. However, I am now interested in finding the SNPs that present among these two genomes. I was suggested with MUMmers and MAUVE. I managed to reorder the contigs with closely related complete genomes from the database using MAUVE. Unfortunately, I can't perform SNPs call using MUMmers since both of my draft genomes contains multiple contigs instead of one as it shows error during the run. I was told that MAUVE can generate pseudogenomes which allows MUMmers to perform side to side genome comparison but I have not idea which data to choose since there are few files being generated by MAUVE. My question is, if there any tools which can generate a pseudo- single contig genomes (like the complete genome sequence) which ease the process of genomic analysis? If no, what are the strategy I should use in order for me to perform SNPs analysis on two draft genomes? My goal of the comparison is to find out the SNPs that present and its respected genes affected. Another question I would like to know is, what is the possible method to create a circular genome using draft genome data? Thank you.
Hello!!!
I am recently planning to work on CNV data analysis on Bladder Cancer. Could you please let me know how shall I find the Bladder cancer CNV data.
It will be more useful if you open a new discussion (question) for you as well as others.