read_info_file

Read the `--info-file` output generated by cutadapt for adapter trimming.
Column structure differs depending on whether the input came from
Nanopore (ONT) or Illumina sequencing.

A series of R functions that come in handy while working with metabarcoding data.
The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way.
In a way it is all about putting together the grammar of the 'tidyverse' from Wickham et al.(2019) <doi:10.21105/joss.01686>
with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) <doi:10.1111/j.1654-1103.2003.tb02228.x>
and 'phyloseq' McMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>.
The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'),
to process 'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file' output. When it comes to sequence counts across samples, the package
works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.

Ramón Gallego Simón

eDNAfuns

Working with Metabarcoding Data in a Tidy Format

read_info_file function

<dl><dt>file</dt>
<dd>Path to the cutadapt info file (TSV).</dd>
<dt>delim</dt>
<dd>Field delimiter (default = "\t").</dd>
<dt>col_select</dt>
<dd>Optional tidyselect specification of which columns to read.</dd>
<dt>...</dt>
<dd>Additional arguments passed to [vroom::vroom()].</dd></dl>

Arguments

Read cutadapt info files — read_info_file

<dl>

<dt>file</dt>
<dd>Path to the cutadapt info file (TSV).</dd>


<dt>delim</dt>
<dd>Field delimiter (default = "\t").</dd>


<dt>col_select</dt>
<dd>Optional tidyselect specification of which columns to read.</dd>


<dt>...</dt>
<dd>Additional arguments passed to [vroom::vroom()].</dd>

</dl>

read_info_file: Read cutadapt info files

Description

Usage

Value

Arguments

Details

Examples