Main command to trim primers using 'Cutadapt' and core 'DADA2' functions

Usage

cut_trim(analysis_setup, cutadapt_path, overwrite_existing = FALSE)

Arguments

analysis_setup: An object containing directory paths and data tables, produced by the prepare_reads function
cutadapt_path: Path to the 'Cutadapt' program.
overwrite_existing: Logical, indicating whether to remove or overwrite existing files and directories from previous runs. Default is FALSE.

Value

Trimmed reads, primer counts, quality plots, and ASV matrix.

Details

If samples are comprised of two different metabarcodes (like ITS1 and rps10), reads will also be demultiplexed prior to 'DADA2'-specific read trimming steps.

Examples

# \donttest{
# Remove remaining primers from raw reads, demultiplex pooled barcoded samples,
# and then trim reads based on specific 'DADA2' parameters
analysis_setup <- prepare_reads(
  data_directory = system.file("extdata", package = "demulticoder"),
  output_directory = tempdir(),
  overwrite_existing = TRUE
)
#> Existing files found in the output directory. Overwriting existing files.
#> Rows: 2 Columns: 25
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): primer_name, forward, reverse
#> dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
#> lgl  (4): already_trimmed, count_all_samples, multithread, verbose
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 2 Columns: 25
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): primer_name, forward, reverse
#> dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
#> lgl  (4): already_trimmed, count_all_samples, multithread, verbose
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 4 Columns: 3
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): sample_name, primer_name, organism
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Creating output directory: /tmp/RtmpBJNmaI/demulticoder_run/prefiltered_sequences

cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)
#> Running cutadapt 3.5 for its sequence data

#> Running cutadapt 3.5 for rps10 sequence data

# }