Faster Short DNA Sequence Alignment with Parallel BWA

Peters, Darren; Qiu, Keni; Liang, Ping

doi:10.1063/1.3663477

Cited by 8 publications

(6 citation statements)

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“…This method reconstructs the history of dynamic changes in population size over time using the distribution of the most recent common ancestor between two alleles in one individual. Paired-end Illumina reads of A. catalpifolium and A. yangbiense were aligned to their reference genomes using BWA-MEM v0.7.10 ( Peters et al 2011 ). Then, the heterozygous biallelic SNPs were called using SAMtools v0.1.19 ( Li et al 2009 ), and reads of very low depth (less than a third of the average depth) or of very high depth (twice the average depth) were removed.…”

Section: Methodsmentioning

confidence: 99%

Whole-Genome Sequencing ofAcer catalpifoliumReveals Evolutionary History of Endangered Species

Zhang

et al. 2021

Genome Biology and Evolution

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Acer catalpifolium is an endangered species restricted to remote localities of West China. Understanding the genomic content and evolution of A. catalpifolium is essential to conservation efforts of this rare and ecologically valuable plant. Here, we report a high-quality genome of A. catalpifolium consisting of ∼654 Mbps and ∼35,132 protein-coding genes. We detected 969 positively-selected genes in two Acer genomes compared with four other eudicots, 65 of which were transcription factors. We hypothesize that these positively-selected mutations in transcription factors might affect their function and thus contribute to A. catalpifolium’s decline-type population. We also identified 179 significantly expanded gene families compared to 12 other eudicots, some of which are involved in stress responses, such as the FRS-FRF family. We inferred that A. catalpifolium has experienced gene family expansions to cope with environmental stress in its evolutionary history. Finally, 109 candidate genes encoding key enzymes in the lignin biosynthesis pathway were identified in A. catalpifolium; of particular note were the large range and high copy number of cinnamyl alcohol dehydrogenase genes. The chromosome-level genome of A. catalpifolium presented here may serve as a fundamental genomic resource for better understanding endangered Acer species, informing future conservation efforts.

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Section: Methodsmentioning

confidence: 99%

Whole-Genome Sequencing ofAcer catalpifoliumReveals Evolutionary History of Endangered Species

Zhang

et al. 2021

Genome Biology and Evolution

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“…The Hi-C reads were processed using the Juicer software (version 1.5) [24]. Brie y, the high-quality Hi-C reads were mapped to the pig reference genome (susScrofa11.1, access date:2021-08-28) using BWA (v0.7.15) [25,26] with default parameters. Unaligned read pairs and PCR duplicates were ltered out using Juicer, and alignments with low quality (MAPQ < 30) were also discarded.…”

Section: Hi-c Data Processing and Tad Callingmentioning

confidence: 99%

A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

Yin,

Zhao,

Yang

et al. 2024

Preprint

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Background Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds. Results Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)—critical growth factors involved in bone and cartilage development. Conclusion Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.

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“…As an example, Bowtie, both versions Bowtie1 and Bowtie2, implements multithreading with Posix Threads. The BWA aligner is implemented in two different versions: multithreads by exploiting a pool of Posix Threads in BWA and by using MPI (message passing interface) to exploit both shared memory and distributed clusters (pBWA [ 15 ]). Posix Threads is also exploited by the BLASR aligner for multithreading.…”

Section: Related Workmentioning

confidence: 99%

Sequence Alignment Tools: One Parallel Pattern to Rule Them All?

Misale

Ferrero

Torquati

et al. 2014

BioMed Research International

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In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all be abstracted to a single parallel paradigm. We compare these tools to their porting onto the FastFlow pattern-based programming framework, which provides programmers with high-level parallel patterns. By using a high-level approach, programmers are liberated from all complex aspects of parallel programming, such as synchronisation protocols, and task scheduling, gaining more possibility for seamless performance tuning. In this work, we show some use cases in which, by using a high-level approach for parallelising NGS tools, it is possible to obtain comparable or even better absolute performance for all used datasets.

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Faster Short DNA Sequence Alignment with Parallel BWA

Cited by 8 publications

References 0 publications

Whole-Genome Sequencing ofAcer catalpifoliumReveals Evolutionary History of Endangered Species

Whole-Genome Sequencing ofAcer catalpifoliumReveals Evolutionary History of Endangered Species

A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

Sequence Alignment Tools: One Parallel Pattern to Rule Them All?

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