Comparative genomics_35 bacterial strains

[buthercup_ch]

Hi everyone,

I'm currently dealing with the comparative analysis of the genome sequence of 35 bacterial strains.
I AM NOT BIOINFORMATICIAN, but a former collaborator in a former project dealing with 7 strains used CD-HIT for clustering the common orthologs, and I was wondering if the same tool could be used to cluster 35 genomes.

Is there any CD-HIT expert that could help me with this issue? If CD-HIT is not the tool…, any other suggestion?

[bioBob]

Hi, it might help to add some detail here. What is the source of your data? NGS? What did you currently have, SNP and INDEL lists or it sounds like you have predicted gene sequences??

[buthercup_ch]

Hi bioBob, thanks for you interest.
The only material I have is a set of 35 genomes in .gb format. Obviously the original data were obtained by HTS in Illumina… ?? I don't know any other details. Some one perform the assembly and annotation and I received the .gb files.
I'm afraid I can't help more than this.