data_for_manuscript_submission.zip

The files and scripts in this zip folder are associated with the manuscript "Adoption of alternative life cycles in a parasitic trematode is linked to microbiome differences" <br> There are four subfolders: 1. 2019 - OG3930P6_fastq: subfolder containing the demultiplexed fastq files from sequencing the 2019 datasets - OG3930P6_qc: subfolder containing the FastQC reports for the 2019 sequences - metadata-3930P6.tsv: metadata associated with the sequences generated for the 2019 dataset 2. 2021 - FASTQ_Generation_2021-06-01_22_13_16Z-423135717: subfolder containing the demultiplexed fastq files from sequencing the 2019 datasets - FASTQC_results.zip: zipped subfolder containing the FastQC reports for the 2021 sequences - metadata-6675P2.tsv: metadata associated with the sequences generated for the 2021 dataset <br> 3. MCS_qc: contains the files required and the result of the quality checks comparing the ZymoBiomics Standard communities with the observed ZymoBiomic communities in the 2019 and the 2021 datasets - 2019observed-species-table-MCS-withBlanks-silva.qza: input for the analyses (2019 observed data) - 2019observed-species-table-MCS-withBlanks-silva.qzv: visualization file of the 2019 input (2019 observed data) - 2021observed-species-table-MCS-withBlanks-silva.qza: input for the analyses (2021 observed data) - 2021observed-species-table-MCS-withBlanks-silva.qzv: visualization file of the 2021 input (2021 observed data) - MCS-expected-table_2021.tsv: expected composition of the mock communities for the 2019 dataset - MCS-expected-table2019.tsv: expected composition of the mock communities for the 2021 dataset - qc-MCS-comparison-withBlanks_2021.qzv: result of the expected-observed comparison of the mock communities for the 2021 dataset - qc-MCS-comparison-withBlanks_2019.qzv: result of the expected-observed comparison of the mock communities for the 2019 dataset <br> 4. merged - merged-clean-filtered-2-500-observed-taxonomy-silva: clean and filtered merged dataset with lower depth - taxonomy data (input for R, output of Qiime2) - merged-clean-filtered-2-500-rep-seqs-silva: clean and filtered merged dataset with lower depth - sequences (input for R, output of Qiime2) - merged-clean-filtered-8-1000-observed-taxonomy-silva: clean and filtered merged dataset with greater depth - taxonomy data (input for R, output of Qiime2) - merged-clean-filtered-8-1000-rep-seqs-silva: clean and filtered merged dataset with greater depth - sequences (input for R, output of Qiime2) - merged-clean-filtered-aligned-2-500-rep-seqs-silva: clean and filtered merged dataset with lower depth - alignment (input for R, output of Qiime2) - merged-clean-filtered-aligned-8-1000-rep-seqs-silva: clean and filtered merged dataset with greater depth - alignment (input for R, output of Qiime2) - merged-clean-filtered-rooted-tree-2-500-rep-seqs-silva: clean and filtered merged dataset with lower depth - rooted tree (input for R, output of Qiime2) - merged-clean-filtered-rooted-tree-8-1000-rep-seqs-silva: clean and filtered merged dataset with greater depth - rooted tree (input for R, output of Qiime2) - merged-clean-filtered-unrooted-tree-2-500-rep-seqs-silva: clean and filtered merged dataset with lower depth - unrooted tree (input for R, output of Qiime2) - merged-clean-filtered-unrooted-tree-8-1000-rep-seqs-silva: clean and filtered merged dataset with greater depth - unrooted tree (input for R, output of Qiime2) - merged-table-clean-filtered-2-500-silva: clean and filtered merged dataset with lower depth - feature table (input for R, output of Qiime2) <br>