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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
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detect 16S indels without references #34

Open roblanf opened 4 years ago

roblanf commented 4 years ago

from: https://github.com/roblanf/sangeranalyseR/issues/32#issuecomment-597974547

@czliobio says:

"Poly peak parser explain what the trace look like when the when a heterozygous indel exist. (https://doi.org/10.1002/dvdy.24183). However, it still needs reference sequence to determine the INDEL. Paper “Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels”(10.1371/journal.pcbi.1000113) might described the closest solution. Besides BCV (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054835) and CASEU (“https://www.ncbi.nlm.nih.gov/pubmed/32114382”) trying to unmixing the poly peaks might be also solutions to separate heterozygous copies and thus detect the indels by alignment. Hope these might help. If test ab1 files are needed, I can collect some in one or two days."

Again, seems like it should be feasible.

czliubio commented 4 years ago

Hi Rob, I collected some indel cases and attach here indel-sample.zip. Hope it might help for testing. sangeranalyseR is really helpful. Thank you very much. Best regards, Kevin