515F/926R mock communities analysis script

We determined the stability of ASV clusters in terms of taxonomy, abundance and phylogeny generated with DADA2 through a variety of trimming tresholds.

Structure of the starting repository

└── Cloned repo  
    ├── 00-raw  
    │   └── raw_reads.fastq.gz  
    ├── in-silico-mocks  
    │   └── 02-EUKs/02-PROKs  
    │          └── Even/Staggered  
                      ├── clone_names.tsv
    │                 └── reads.fastq  
    ├── generate_data.sh
    ├── run_analysis.ipynb
    ├── environment.yml
    ├── MANIFEST.tsv
    └── METADATA.tsv

Datasets

Dataset	Community	Number of clones	Link
16S	Even	11	https://www.ebi.ac.uk/ena/browser/view/PRJEB48162
16S	Staggered	27	https://www.ebi.ac.uk/ena/browser/view/PRJEB48162
18S	Even	10	https://www.ebi.ac.uk/ena/browser/view/PRJEB35673
18S	Staggered	16	https://www.ebi.ac.uk/ena/browser/view/PRJEB35673

Generate the data

Run generate_data.sh from the cloned repo, then open the run_analysis.ipynb jupyter notebook and run all.

Final repository

└── Cloned repo  
    ├── 00-raw  
    │   └── raw_reads.fastq.gz  
    ├── 01-trimmed  
    │   └── trimmed_reads.fastq  
    ├── 02-EUKs/02-PROKs  
    │   ├── 00-fastq  
    │   │   └── cdhit_euk_reads.fastq  
    │   ├── intermediate_files  
    │   │   ├── all_taxonomies  
    │   │   │   ├── Even/Staggered
    │   │   │   │     └── Taxonomies.tsv  
    │   │   └── all_trims  
    │   │       └── Forward and reverse trim combinations  
    │   │             └── 03-DADA2d  
    │   │                 ├── denoising_statistics.qza  
    │   │                 ├── representative_sequences.qza  
    │   │                 ├── table.qza  
    │   │                 └── taxonomy  
    │   │                      └── classification.qza  
    │   └── logs  
    ├── in-silico-mocks  
    │   └── 02-EUKs/02-PROKs  
    │          └── Even/Staggered  
    |                 ├── clone_names.tsv
    │                 ├── reads.fastq  
    │                 └── taxonomy  
    │                      └── classification.qza     
    ├── generate_data.sh
    ├── run_analysis.ipynb
    ├── environment.yml
    ├── MANIFEST.tsv
    └── METADATA.tsv