Hi,
I was hoping someone here could point me in the direction of a good tool for calculation of pan and core genomes in prokaryotes! I am looking for one or several tools/scripts that does a number of things:
I have a bucket full of bacterial genome data (in contigs mostly) of the same species and would like, based on various gropings of these, to determine initially overall pan and core genomes of the isolates.
Besides getting just the number of genes in each group, it would also be very beneficial to some sort if genes list output for further analysis.
Finally, I would like to see what difference there is between the calculated core/pan genome in 1 group compared to another defined set of isolates in another group - again not only a number of genes but an actual list of genes or gene sequences.
The contigs have not been analysed for CDSs or annotated in any way, but this I can do in another pipeline prior to the pan core calculation if needed.
Thanks!!!
I was hoping someone here could point me in the direction of a good tool for calculation of pan and core genomes in prokaryotes! I am looking for one or several tools/scripts that does a number of things:
I have a bucket full of bacterial genome data (in contigs mostly) of the same species and would like, based on various gropings of these, to determine initially overall pan and core genomes of the isolates.
Besides getting just the number of genes in each group, it would also be very beneficial to some sort if genes list output for further analysis.
Finally, I would like to see what difference there is between the calculated core/pan genome in 1 group compared to another defined set of isolates in another group - again not only a number of genes but an actual list of genes or gene sequences.
The contigs have not been analysed for CDSs or annotated in any way, but this I can do in another pipeline prior to the pan core calculation if needed.
Thanks!!!
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