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Sabre - Single-cell reAd-Backed umi-awaRE phasing

What is Sabre

Single-cell level haplotype phasing is key to studying clonal hematopoiesis, X chromosome inactivation, RNA editing, mitotic recombination, and somatic mutations. The availability and exponential growth of scRNA-seq data represent a vastly untapped resource for read-backed phasing in single cells. Unlike bulk RNA-seq, scRNA-seq’s read structure, high PCR duplication, and low sequencing depth present challenges. We introduce Sabre, a method that accurately infers long-range haplotypes by leveraging the read structure and PCR duplicates unique to scRNA-seq data. Sabre can be utilized in these following three scenarios:

• Germline variants, where all cells share the same haplotypes;
• Somatic variants, where haplotypes are shared by mutant cells and their progenies;
• RNA editing variants, where haplotypes are unique to each cell. Sabre uses ultrafast graph algorithms and is scalable to atlas-scale data with 1M single cells.

Developed and maintained by Laurentius.

Runs on python 3.x, requires samtools, vcftools, bedtools.