cytozip: index-free, chunk-compressed storage for scalable single-cell DNA methylation analysis
A scalable, cloud-native ecosystem for single-cell and population DNA methylation analysis
Installation
conda
https://anaconda.org/bioconda/cytozip
mamba install -c wubinding -c bioconda cytozip
# or
conda install -c wubinding -c bioconda cytozip
# -c wubinding is optional, which may be the latest version
pip
# Prerequisites (one of):
conda install -c bioconda htslib libdeflate samtools # recommended
# apt-get install libhts-dev libdeflate-dev samtools # Debian/Ubuntu
# brew install htslib libdeflate samtools # macOS
pip install cytozip
# or reinstall
pip uninstall -y cytozip && pip install git+http://github.com/DingWB/cytozip
Implementation
| allcools | ballcools | cytozip | |
|---|---|---|---|
| Format | .tsv.gz | .ballc | .cz |
| Compression algorithm | bgzip | bgzip | cytozip |
| Support Random Access ? | Yes | Yes | Yes |
| Need extra index file for query? | Yes | yes | No |
| Quickly Merge? | No | No | Yes |
Usage
Example dataset
https://figshare.com/articles/dataset/cytozip_example_data/32095567
1 maintainer
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Source Distribution
cytozip-0.3.9.tar.gz
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