Quick Start Guide

This page provides simple quick-start information for using sangeranalyseR with .ab1 files. Please read the Beginners Guide page for more details on each step.

If you haven't already, please follow the steps in the Installation page to install and load sangeranalyseR.


Super-Quick Start (3 lines of code)

The most minimal example gets the job done in three lines of code. More details below.

my_aligned_contigs <- SangerAlignment(parentDirectory     = "./my_data/",
                                      suffixForwardRegExp = "_[0-9]+_F+",
                                      suffixReverseRegExp = "_[0-9]+_R +")

writeFasta(my_aligned_contigs)

generateReport(my_aligned_contigs)

Step 1: Prepare your input files

Put all your AB1 files in a directory ./my_data/. The directory can be called anything.

Name your files according to the convention contig_index_direction.ab1. E.g. Drosophila_COI_1_F.ab1 and Drosophila_COI_2_R.ab1 describes a forward and reverse read to assemble into one contig. You can have as many files and contigs as you like in one directory.


Step 2: Load and analyse your data

my_aligned_contigs <- SangerAlignment(parentDirectory     = "./my_data/",
                                      suffixForwardRegExp = "_[0-9]+_F+",
                                      suffixReverseRegExp = "_[0-9]+_R +")

This command loads, trims, builds contigs, and aligns contigs. All of these are done with sensible default values, which can be changed. I


Step 3 (optional): Explore your data

launchApp(my_aligned_contigs)

This launches an interactive Shiny app where you can view your analysis, change the default settings, etc.


Step 4: Output your aligned contigs

writeFasta(my_aligned_contigs)

This will save your aligned contigs as a FASTA file.


Step 5 (optional): Generate an interactive report

generateReport(my_aligned_contigs)

This will save a detailed interactive HTML report that you can explore.


For more detailed analysis steps, please choose one the following topics :