Welcome to DECARD (Detailed Evaluation Creation and Analysis of Read Data).
DECARD can be used to simulate amplicon-based microbiome experiments, and test how classification software performs. DECARD can help with each step of the process:
- Downloading references sequences from NCBI (NCBI_16SMicrobial_update.py) and SILVA (SILVA_selectFromGenera.py)
- Curating the reference sequences by GENUS and SPECIES. (selectFromGenera.py)
- Performing quality control on the reference (genera_qc.py)
- Generate targets for a set of communities (generate_targets.py)
- Perform in-silico PCR and generate amplicon sequences (generate_sequences.py)
- (Optional). Perform in-silico sequencing of the amplicons, with error addition using something like ART
These amplicons or sequences can then be classified. The resultant classifications can be evaluated
- For the accuracy of the OTU generation step (test_otu.py)
- For the resolution and accuracy of the classification of each source organism (test_classification.py)
- Version 0.1
One can download a working and fully installed version of decard in a docker container at: https://hub.docker.com/r/golob/decard/ At that site is a tutorial to guide you through using decard.