fasta_reader

fastq_reader

Functions to read sequence files into a tidy data frame with one row per sequence.

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

fasta_reader function

<dl><dt>path_to_fasta</dt>
<dd>Character. Path to a FASTA file.</dd>
<dt>path_to_fastq</dt>
<dd>Character. Path to a FASTQ file.</dd>
<dt>keepQ</dt>
<dd>Logical. If `TRUE`, keep a third column with quality scores when
reading FASTQ files. Default is `FALSE`.</dd></dl>

Arguments

Read FASTA or FASTQ files into a tibble — fasta_reader

<dl>

<dt>path_to_fasta</dt>
<dd>Character. Path to a FASTA file.</dd>


<dt>path_to_fastq</dt>
<dd>Character. Path to a FASTQ file.</dd>


<dt>keepQ</dt>
<dd>Logical. If `TRUE`, keep a third column with quality scores when
reading FASTQ files. Default is `FALSE`.</dd>

</dl>

fasta_reader: Read FASTA or FASTQ files into a tibble

Description

Usage

Value

Arguments

Examples