Additional information for manuscript entiteld "Host-parasitoid associations in marine planktonic time series: can metabarcoding help reveal them?" (PONE-D-20-17825R1)

<p><strong>Description:</strong></p> <p>This repository contains material to reproduce metabarcoding analyses based on the q-zip pipeline (https://github.com/PyoneerO/qzip). Raw fastq files can be downloaded from https://www.ebi.ac.uk/ena/browser/view/PRJEB37135. The used reference file can be downloaded from https://github.com/pr2database/pr2database/releases/tag/4.11.1. Please select the files created for the classifier implemented in mothur.</p> <p>The dockerfile in this repository can be used to set up the environment which inludes the installation of the needed versions of the needed tools.</p> <p>Twelve different analyses had been conducted. For each analysis one zip file had been created which contains the following files:</p> <p>- q-zip_commands.sh: the shell script to launch the pipeline</p> <p>- q-zip_parameters.txt: pipeline parameter file as input of the shell script</p> <p>- q-zip_workflow.log: log file containing stdout and sdterr</p> <p>- q-zip_seq_of_coms.txt: file containing each command executed during the pipeline run (minimal set of command to reproduce the results)</p> <p>- seq_number_stats.txt: file containing the sequence numbers at each filtering step</p> <p>- OTU tables in tsv and biom format (sequences and taxonomic annotation included)</p> <p>- Meta data map (here only including the raw file names)</p> <p>- swarm sequences in fasta format</p> <p>&nbsp;</p> <p><strong>The following analyses had been conducted:</strong></p> <p>- otu formation at swarm distance 1; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 5; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 10; default settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; relaxt settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 2; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 3; strict settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p>- otu formation at swarm distance 1; very strict settings settings for preceding sequence filtering and subsequent taxonomic annotation</p> <p><strong>Settings into more detail:</strong></p> <p>relaxt settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 3 bp - threshold of average quality within of 5</li> <li>vsearch paired-end merging: length of minimum overlap of 25 bp - number of mismatches allowed of 5 bp</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 75% - percentage mismatches allowed of 20%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.6</li> </ul> <p>default settings (used for the manuscript):</p> <ul> <li>trimmomatic filtering: sliding window length of 3 bp - threshold of average quality within of 8</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 5</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 90% - percentage mismatches allowed of 10%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.25 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.8</li> </ul> <p>strict settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 1 bp - threshold of average quality within of 15</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 0</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 90% - percentage mismatches allowed of 10%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.9</li> </ul> <ul> </ul> <p>very strict settings:</p> <ul> <li>trimmomatic filtering: sliding window length of 1 bp - threshold of average quality within of 15</li> <li>vsearch paired-end merging: length of minimum overlap of 50 bp - number of mismatches allowed of 0</li> <li>cutadapt primer removal: percentage primer to sequence overlap of 100% - percentage mismatches allowed of 0%</li> <li>vsearch eeMax filtering: max number of errors expected per sequence of 0.1 bp</li> <li>minimum sequence length of 300 bp and maximum sequence length of 550 bp</li> <li>mothur classification cutoff (refers to confidence threshold of NBC) of 0.9</li> </ul>