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sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R


sangeranalyseR is feature-rich, free, and open-source R package for processing Sanger sequencing data. It allows users to go from loading reads to saving aligned contigs in a few lines of R code by using sensible defaults for most actions. It also provides complete flexibility for determining how individual reads and contigs are processed, both at the command-line in R and via interactive Shiny applications. sangeranalyseR provides a wide range of options for all steps in Sanger processing pipelines including trimming reads, detecting secondary peaks, viewing chromatograms, detecting indels and stop codons, aligning contigs, estimating phylogenetic trees, and more. Input data can be in either ABIF or FASTA format. sangeranalyseR comes with extensive online documentation and outputs aligned and unaligned reads and contigs in FASTA format, along with detailed interactive HTML reports. sangeranalyseR supports the use of colorblind-friendly palettes for viewing alignments and chromatograms. It is released under an MIT licence and available for all platforms on Bioconductor (, last accessed February 22, 2021) and on Github (, last accessed February 22, 2021).

Type Journal
ISBN 1759-6653 (Electronic) 1759-6653 (Linking)
Authors Chao, K. H.; Barton, K.; Palmer, S.; Lanfear, R.
Publisher Name Genome Biology and Evolution
Published Date 2021-03-31
Published Volume 13
Published Issue 3
Status Published in-print
DOI 10.1093/gbe/evab028
URL link to publisher's version