Therefore, it is important to have a consistent naming strategy. For those having the same “contig name” will be grouped into the same contig. Then, sangeranalyseR uses the str_split function to split and vectorize their filenames into “contig name” and “direction-suffix” two parts. So how sangeranalyseR works is that it first matches the forward and reverse reads by matching REGEX_SuffixForward and REGEX_SuffixReverse. Here is an example of how it works in sangeranalseR: Please refer to What is a regular expression? for more details. If you don’t know what regular expression is, don’t panic - it’s just a way of recognising text. REGEX_SuffixReverse: this is a regular expression that matches all filenames in reverse direction.REGEX_SuffixForward: this is a regular expression that matches all filenames in forward direction.We suggest users to put only target AB1 files inside this directory and do not include any other unrelated files.
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ABIF_Directory: this is the directory that contains all AB1 files, and it can be either an absolute or relative path.Advanced User Guide - SangerAlignment ( FASTA).Advanced User Guide - SangerContig ( FASTA).Advanced User Guide - SangerRead ( FASTA).(6) Generating SangerAlignment report (AB1).(5) Writing SangerAlignment FASTA files (AB1).(4) Launching SangerAlignment Shiny app (AB1).(3) Updating SangerAlignment quality trimming parameters (AB1).(2.2) “CSV file matching” SangerAlignment creation ( AB1).(2.1) “Regular Expression Method” SangerAlignment creation ( AB1).(2) Creating SangerAlignment instance from AB1.(1) Preparing SangerAlignment AB1 inputs.Generating SangerAlignment report (AB1).Writing SangerAlignment FASTA files (AB1).Updating SangerAlignment quality trimming parameters.(2) “CSV file matching” SangerAlignment creation ( AB1).(1) “regular expression matching” SangerAlignment creation ( AB1).Creating SangerAlignment instance from AB1.
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