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roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R
MIT License
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SangerContig: support for non-coding references #90

Open nick-youngblut opened 1 year ago

nick-youngblut commented 1 year ago

At least for sangerseqR_1.34.0, one can provide a reference for SangerContig(), but it must be an amino acid sequence (refAminoAcidSeq=), so non-coding genes (e.g., 16S rRNA) are not supported. It would be helpful to enable DNA sequence references.

Also, one cannot pass certain arguments to DECIPHER::AlignSeqs() from SangerContig() such as iterations and refinements. This feature would be helpful for potentially improving alignments.

Kuanhao-Chao commented 1 year ago

Hi @nick-youngblut, thank you for your valuable feedback and bug reports; we genuinely appreciate your contributions.

sangeranalyseR has not been actively maintained for some time, but now I'm considering adding these features and planning for a stable release.

If you'd like to get involved, please feel free to open a pull request, and we can collaborate on implementing these improvements. I'll keep you updated on our progress.