Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications

Abstract

The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs)—sequence differences between paralogous sequences—to distinguish between multiple alignment locations. On simulated datasets, DuploMap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3–90.6%) and BLASR (82.9–90.7%) while maintaining high precision. Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8–21% of the reads in segmental duplications with high confidence relative to Minimap2. Using DuploMap-aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence was mappable, variant calling achieved a higher F1 score and 14 713 additional variants supported by linked-read data were identified. Finally, we demonstrate that a significant fraction of PSVs in segmental duplications overlaps with variants and adversely impacts short-read variant calling.

Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering

“…4a ). However, it was challenging to identify the exact location of the duplicated region based on the sequencing data due to the short read length of Illumina sequencing 50 , 51 . We thus deleted the original region of PP_5050–PP_5242 in QP478, using the known sequences outside the region as homologous arms, to generate LC171, and deleted a portion of the duplication from PP_5084–PP_5242 to generate strain LC173.…”

Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment

“…Finally, we note that Vulcan could be used for any combination of long-read mappers that output the edit distance (NM tag) directly within sam/bam file output. Thus, allowing the inclusion of WinnowMap [ 39 ], LAST [ 21 ], LRA [ 23 ], or Duplomap [ 40 ] may further exploit our observation that variable gap costs for different read-to-reference mappings provide improved SV calling while offering improved runtimes compared to the more computationally expensive long-read mapping approaches.…”

Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP

“…Collapsed duplication FP regions and population CNV FP regions are both related to collapsed duplications errors in the GRCh38, recently identified and corrected by the T2T consortium [23]. These regions are populated with paralog-specific variants (PSV)-variation among paralogous sequences, which impact short-read variant calling [24]. In addition, the long segmental duplications with high sequence identity are a challenge for long-read mapping accuracy [24].…”

“…These regions are populated with paralog-specific variants (PSV)-variation among paralogous sequences, which impact short-read variant calling [24]. In addition, the long segmental duplications with high sequence identity are a challenge for long-read mapping accuracy [24]. Therefore, we found lower SNPs F1 scores using only ONT or Illumina data (collapsed duplication FP regions for either ONT or Illumina: 0.7797, 0.4263; population CNV FP regions: 0.9115, 0.7720).…”