Automatic detection and subtyping of CRISPR-Cas operons
Project description
CasPredict
Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.
This software finds Cas genes with a large suite of HMMs, then groups these HMMs into operons, and predicts the subtype of the operons based on a scoring scheme. Furthermore, it finds CRISPR arrays with minced, and using a kmer-based machine learning approach (extreme gradient boosting trees) it predicts the subtype of the CRISPR arrays based on the consensus repeat. It then connects the Cas operons and CRISPR arrays, producing as output:
- CRISPR-Cas loci, with consensus subtype prediction based on both Cas genes (mostly) and CRISPR consensus repeats
- Orphan Cas operons, and their predicted subtype
- Orphan CRISPR arrays, and their predicted associated subtype
It includes the following subtypes:
- All the ones in the most recent Nature Reviews Microbiology: Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
- Updated type IV subtypes and variants based on: Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids
- Type V-K: RNA-guided DNA insertion with CRISPR-associated transposases
- Transposon associated type I-F: Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration
Table of contents
Quick start
conda create -n caspredict -c conda-forge -c bioconda -c russel88 caspredict
conda activate caspredict
caspredict my.fasta my_output
Installation
Conda
It is advised to use miniconda or anaconda to install.
Create the environment with caspredict and all dependencies
conda create -n caspredict -c conda-forge -c bioconda -c russel88 caspredict
pip
If you have the dependencies (Python >= 3.8, HMMER >= 3.2, Prodigal >= 2.6, grep, sed) in your PATH you can install with pip
python -m pip install caspredict
When installing with pip, you need to download the database manually:
Coming soon...
CasPredict - How to
CasPredict takes as input a nucleotide fasta, and produces outputs with CRISPR-Cas predictions
Activate environment
conda activate caspredict
Run with a nucleotide fasta as input
caspredict genome.fa my_output
Use multiple threads
caspredict genome.fa my_output -t 20
Check the different options
caspredict -h
Output
- CRISPR_Cas.tab: CRISPR_Cas loci, with consensus subtype prediction
- CRISPR_Cas_putative.tab: Putative CRISPR_Cas loci, often lonely Cas genes next to a CRISPR array
- cas_operons.tab: All certain Cas operons
- crisprs_all.tab: All CRISPR arrays
- crisprs_orphan.tab: Orphan CRISPRs (those not in CRISPR_Cas.tab)
- cas_operons_orphan.tab: Orphan Cas operons (those not in CRISPR_Cas.tab)
- cas_operons_putative.tab: Putative Cas operons, mostly false positives, but also some ambiguous and partial systems
- spacers/*.fa: Fasta files with all spacer sequences
- hmmer.tab: All HMM vs. ORF matches, raw unfiltered results
- arguments.tab: File with arguments given to CasPredict
Notes on output
Files are only created if there is any data. For example, the crisprs_orphan.tab file is only created if there are any orphan CRISPR arrays.
RepeatType - How to
With an input of CRISPR repeats (one per line, in a simple textfile) RepeatType will predict the subtype, based on the kmer composition of the repeat
Activate environment
conda activate caspredict
Run with a simple textfile, containing only CRISPR repeats (in capital letters), one repeat per line.
repeatType repeats.txt
Output
The script prints:
- Repeat sequence
- Predicted subtype
- Probability of prediction
Notes on output
- Predictions with probabilities below 0.75 are uncertain, and should be taken with a grain of salt.
- The classifier was only trained on the subtypes for which there were enough (>20) repeats. It can therefore only predict subtypes of repeats associated with the following subtypes:
- I-A, I-B, I-C, I-D, I-E, I-F, I-G
- II-A, II-B, II-C
- III-A, III-B, III-C, III-D
- IV-A1, IV-A2, IV-A3
- V-A
- VI-B
- This is the accuracy per subtype (on an unseen test dataset):
- I-A 0.60
- I-B 0.90
- I-C 0.98
- I-D 0.47
- I-E 1.00
- I-F 0.99
- I-G 0.83
- II-A 0.94
- II-B 1.00
- II-C 0.89
- III-A 0.89
- III-B 0.49
- III-C 0.60
- III-D 0.28
- IV-A1 0.79
- IV-A2 0.78
- IV-A3 0.98
- V-A 0.77
- VI-B 1.00
Project details
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