Add a new tutorial explaining how to use breseq to locate a generic integration cassette in a genome.
Use Acinetobacter baylyi ADP1 data and the tdk-Kan cassette as an example.
Show results without providing the cassette reference, with providing it as part of a plasmid, and with annotating it as a repeat_region so it is resolved into a mutation.
There might be some coding to do here to improve things. It would be even better to support prediction of an INT versus a MOB, perhaps depending on how the region was annotated. Maybe features named gene_cassette or integration_cassette or something similar can map to this kind of mutation. Having the distinction could help with mutation counting, screening, etc. Right now, INT mutations must be manually annotated.
Add a new tutorial explaining how to use breseq to locate a generic integration cassette in a genome.
Use Acinetobacter baylyi ADP1 data and the tdk-Kan cassette as an example.
Show results without providing the cassette reference, with providing it as part of a plasmid, and with annotating it as a
repeat_regionso it is resolved into a mutation.There might be some coding to do here to improve things. It would be even better to support prediction of an
INTversus aMOB, perhaps depending on how the region was annotated. Maybe features namedgene_cassetteorintegration_cassetteor something similar can map to this kind of mutation. Having the distinction could help with mutation counting, screening, etc. Right now,INTmutations must be manually annotated.