What Package would you suggest to represent sequence alteration events?


I am looking for a package that would allow me to represent changes to a sequence. Is there something like that around? I looked at GenomeGraph and PopGen (and PopGenSim) but their documentation is quite sparse to understand what is actually going on.

Any suggestions?

Thank you


Maybe this is what your looking for?

I haven’t done any bioinformatics in Julia yet. but I likely will in the near future, so I’d be glad to hear what packages you use in the end.

It depends which types of alteration you’re speaking about, but usually mutations are represented by a genomic position, the reference sequence at that position, and the alternative sequence, plus some other metadata. The standard format for that is VCF, but if you don’t need to read/write vcf files you could use a named tuple or even a dataframe.

1 Like

Definitely not - the Bio.jl monorepo is deprecated. That module is now BioSequences.jl, but you may also want BioAlignments.jl?


Googling Julia can be a bit of a minefield. Took me a while to figure out that I was often reading the docs of older versions of packages etc.


Yeah, that’s a common experience :persevere:. There have been efforts/intentions to throw warnings on older docs versions, though I don’t know how far along they are.

Thank you. Yep. Roundtripping VCFs and BCFs will be useful, but that is not quite what I am after. I want to create a simulator for evolutionary processes.

I decided to cook up something as a learning experience.

I will kee you posted.

I did get that feeling. :expressionless: