Add a tutorial for how to predict genomic insertions of a cassette.

[jeffreybarrick]

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.

[NataliyaTeteneva]

Dear Mr Barrick,

I'm currently trying to do exactly this (to map transposon insertions in the genome). However, I face some problems. Could you please give me an advice how to solve them?

1. With one junction-only-reference (that contains my desired sequence and antibiotic cassette) my breseq run is finished without errors but it does not find any insertions. Actually, in the output it says that 0% of the reads are aligned to my desired sequence (which is not true, I've checked it manually). I tried both consensus and polymorphism modes but neither of them finds the insertions.

2. With the shorter junction-only-reference (that contains only my desired sequence) breseq just crashes with a fatal error and says it's because of the segmentation fault.

I guess that the problem is in my GenBank files that I provide as the junction-only-reference but I cannot figure out what exactly is wrong with them. Could you please give an example how a GenBank file should look like for this task?

Best regards and thank you in advance,
Nataliya Teteneva