cellsnp-lite

cellsnp-lite performs genotyping by piling up expressed alleles and analyzing single-cell and bulk RNA-seq, DNA-seq, and ATAC-seq data to enable genetic analyses.

Key Features:

• Pileup of expressed alleles: Originally developed to pile up expressed alleles from RNA-seq data for downstream genotyping analyses.
• Implementation: Implemented in C/C++ and built on the htslib package to integrate with standard bioinformatics formats and workflows.
• Computational performance: Optimized for improved computational speed and memory efficiency for large-scale single-cell datasets.
• Platform compatibility: Supports both droplet-based and well-based single-cell sequencing platforms and can be applied to bulk and single-cell data.
• Result concordance: Produces results with high concordance compared to existing genotyping methods.

Scientific Applications:

• Donor deconvolution: Enables assignment of cells to donors in multiplexed single-cell RNA-seq and can be integrated with tools such as vireo for doublet detection.
• Genetic analysis: Supports a range of genetic analyses on single-cell and bulk sequencing data across RNA-seq, DNA-seq, and ATAC-seq modalities.

Methodology:

Implemented in C/C++ and built on htslib, cellsnp-lite performs allele pileup from sequencing reads and is optimized for computational speed and memory efficiency.