Main command to trim primers using Cutadapt and core DADA2 functions. If samples contain pooled barcodes, reads will also be demultiplexed

Main command to trim primers using Cutadapt and core DADA2 functions. If samples contain pooled barcodes, reads will also be demultiplexed

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.

Examples

# 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(),
  tempdir_path = tempdir(),
  tempdir_id = "demulticoder_run_temp",
  overwrite_existing = TRUE
)
#> Rows: 2 Columns: 22
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): primer_name, forward, reverse
#> dbl (16): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
#> lgl  (3): already_trimmed, 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: 22
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): primer_name, forward, reverse
#> dbl (16): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
#> lgl  (3): already_trimmed, 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/Rtmp23cMn7/demulticoder_run_temp/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