I am having trouble using Biostrings. I need to locate a section of a specific scaffold by position in my genome assembly and remove it then save as two separate scaffolds. I am not sure how to do this using BioSstrings, if its even possible.

Thanks

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It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing BSgenome package, you can do it like this.

> library(BSgenome.Hsapiens.UCSC.hg38)
>  getSeq(Hsapiens, GRanges(c("chr1:12345-54321","chr2:12345-55555")))
 DNAStringSet object of length 2:
     width seq
 [1] 41977 TCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAG...ACATACTTTTTTCATGTATTTGTTTCTACTGCT
 [2] 43211 AACAATAATAGTCTTACTTTGATTATGATCAAAA...TTGGTCAAAACAACTCTGGGTAAAGACTTTAGG