Hello! I am working with sanger sequences where half of them are in the ab1/abi format, the other half is scf. I am using sangeranalyseR, an R package (https://github.com/roblanf/sangeranalyseR), to do quality-trimming and alignment of my ab1 files, and all seemed to have worked fine. The only issue is that sangeranalyseR only accepts files in the ab1/abi format. I tried converting my scf files to ab1 using a variety of software (e.g. Geneious, staden) and unfortunately the output files are never properly formatted. I noticed that sangeranalyseR uses a function called "read.abif" borrowed from the R package sangerseqR. The same package, sangerseqR, also has a function for reading SCF files and I was wondering if you could help me figuring out a way to manually change sangeranalyseR to use the scf files reader from sangerseqR. It seems like it wouldn't be too difficult to just replace one function with the other. Any other advice would also be greatly appreciated.
