Spectre - Long-read CNV Caller

Spectre is a long-read copy number variation (CNV) caller designed to detect large CNVs (>100kb).

Ont-spectre is a tool based on the original Spectre v0.2.0, with the following main enhancements:

• Diploid Coverage Estimation: Bins containing heterozygous SNVs are used to estimate the properties of the diploid coverage distribution, aiding in the selection of appropriate parameters.
• Karyotype Prediction: Adds sex chromosome karyotype prediction (including XO, XXY, etc). All events are called relative to the predicted karyotype.

Installation

The recommended way to install Spectre is through either pip or conda:

pip install ont-spectre

(or)

conda install nanoporetech::ont-spectre

Note: Spectre supports Python versions >= 3.8.

Build from Source

To install the ont-spectre tool from the source, follow these steps:

1. Clone the repository:

   git clone https://github.com/epi2me-labs/ont-spectre.git
   cd ont-spectre
   

2. Create a virtual environment (optional):

   It’s recommended to use a isolated environment to manage dependencies. Create and activate one with:

   python3 -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate
   

   Alternatively, you can create a conda environment:

   conda create -n spectre python=3.8 pip -y
   conda activate spectre
   

Note: Spectre supports Python versions >= 3.8.

3. Install dependencies and the tool:

   pip install .
   

4. Verify installation:

   After installation, you should be able to run the tool using the entry point spectre:

   spectre --help
   

How to run

Spectre requires the following inputs:

• The output directory of mosdepth, a tool for fast coverage calculation.
• The reference genome (can be bgzip-compressed).
• The window size used in Mosdepth (Ensure that the binsize between Mosdepth and Spectre matches. We suggest a binsize of 1,000 base pairs).
• A VCF file containing SNVs (Single Nucleotide Variants).

Example Command:

spectre CNVCaller \
  --bin-size 1000 \
  --coverage mosdepth/sampleid/ \
  --sample-id sampleid \
  --output-dir sampleid_output_directory_path/ \
  --reference reference.fasta.gz \
  --snv sampleid.vcf.gz

Help

Licence and Copyright

© 2024- Oxford Nanopore Technologies Ltd.

ont-spectre is distributed under the terms of the Oxford Nanopore Technologies Public License v1.0.

Research Release

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.