sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data

Abstract

Profiling gametes of an individual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologies. However, haplotyping single gametes from high-throughput single-cell DNA sequencing datasets using existing methods requires intensive processing. Here we introduce an efficient software toolset using modern programming languages for the common tasks of haplotyping haploid gamete genomes and calling crossovers (sgcocaller), and constructing and visualising individualised crossover landscapes (comapr) from single gametes. With additional data pre-possessing, the tools can also be applied to bulk sequenced samples.

Fancm regulates meiotic double-strand break repair pathway choice in mammals

“…1c). To call crossovers using single-sperm sequencing data and downstream analyses, we developed an open-source bioinformatic tool kit containing sgcocaller and comapr [76] (see Materials and Methods). Consistent with the bulk sequencing and PCR-based methods, an increase in total crossover frequency and map length was observed in Fancm Δ 2/ Δ 2 compared to Fancm +/+ (p = 0.001, permutation test (B = 1,000), 1,347 cM and 1,178 cM, respectively)(Fig.…”

“…Output files from sgcocaller are further parsed and analysed for crossover interval identification and crossover profile comparison. With the sequence of hidden states inferred, the crossover interval locations were called by applying functions implemented in R package comapr [76]. The construction of genetic distance maps and crossover distributions were also performed using comapr .…”

“…Crossover detection from the singlesperm sequencing data was also by applying HMM but with different HMM configurations. Allele read counts for single cells were obtained using customized software tool sgcocaller [76] that summaries the allele counts across all cells and SNP positions into count matrices per sample and crossovers were called with options -cmPmb 0.0001 -maxDP 6 -maxTotalDP 30 .…”

IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells

“…We demonstrated that IIIandMe , which applies to genomic data of high quality, can accurately infer chromosomal haplotypes using three or a few more single gametes and is computationally much more efficient than Hapi . Given that crossovers are very rare (Beye et al 2006; Lyu et al 2022), three gametes are theoretically sufficient for phasing the entire genome, likely pushing the boundary to its possible limit. We foresee that IIIandMe will find its way to become impactful in many genetic research areas and applications.…”

SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing

“…Sperm can be used with genomic technologies to study diverse topics such as fertility, genome structure and forensic science [1][2][3][4][5]. A major challenge for the isolation of individual haploid cells from males for sequencing is that they stick to most pipette tips and tubes, and traditional methods for bulk sperm isolation use technically challenging density gradients.…”