Hi all I have not much knowledge on bioinformatics so need your valuable suggestions in my work I have carried out a whole genome metagenome sequencing of a tissue sample (clinical sample) in this I have got a bacterial organism which is present as 82% among all the bacterial sequences present. I want to get the genome sequence of the target bacteria and carry out further analysis on it. one of my friend helped me in extracting the target genome sequence he has given me a BAM file of the organism from the raw reads and using IGV we could see there is 98.3% coverage with reference geneome sequence.
Can any one guide me how to extract the geneome sequence information from the raw reads or bam file and how to submit it to databases.
Also how to compare the obtained genome sequence with already published genome sequences.
I have no previous experience with Linux based bioinformatics softwares so kindly suggest using windows based website or softwares for this work.
Kindly give your suggestions in this regard Thanks Dr. S. Rajagunalan
