My research work is involved in using next-generation sequencing reads to align to the bacterial genome. Since many bacterial genomes are cyclic, did anyone have such experience to efficiently align reads to circular genome? Thanks
As far as I know deposited genomes are always in linear form . You can not deposite it in a circular form, that is in essential a direct repeat between the. beginning and the end of the contig.
So just use normal alignes like BWA or BOWTIE2 to align your sequences againts the genome.
All the best
Dear Zhang,
Bacterial genomes are circular in nature, but to submit in the ncbi you will submitting only linear form only.
You can check the circularity capicity by analysing your genome with online tools like
CG Viewer http://stothard.afns.ualberta.ca/cgview_server/
and many other linux based tools are available online.
The Geneious mapper and de novo assembler can handle circular genomes by allowing reads to span the origin of your sequence. Reads that align to the beginning and end of the linear genome will be wrapped around, allowing you to get a circular consensus sequence.
See http://geneious.com/features for more information
http://geneious.com/features
I have got sequenced a new bacterial genome, but i want to know whether any putative plasmid is present or not in whole genome. I tried plasmid finder but database of plasmid finder web based server is not sufficient to find out any putative plasmid.So, is there option to know about plasmid in whole genome of bacteria.
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