提高 minimap2 比对准确性的新策略。
New strategies to improve minimap2 alignment accuracy.
机构信息
Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA.
出版信息
Bioinformatics. 2021 Dec 7;37(23):4572-4574. doi: 10.1093/bioinformatics/btab705.
Abstract
SUMMARY
We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100 kb by default, addressing major weakness in minimap2 v2.18 or earlier.
AVAILABILITY AND IMPLEMENTATION
摘要
摘要
我们介绍了 minimap2 的几个最新改进，minimap2 是一种用于核苷酸序列的通用比对工具。现在，minimap2 v2.22 可以更准确地将长读段映射到高度重复的区域，并通过默认的 100kb 以内的插入或缺失来进行对齐，从而解决了 minimap2 v2.18 或更早版本中的主要弱点。
可用性和实现
相似文献
1
New strategies to improve minimap2 alignment accuracy.提高 minimap2 比对准确性的新策略。
Bioinformatics. 2021 Dec 7;37(23):4572-4574. doi: 10.1093/bioinformatics/btab705.
2
Minimap2: pairwise alignment for nucleotide sequences.Minimap2：核苷酸序列的两两比对。
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191.
3
HQAlign: aligning nanopore reads for SV detection using current-level modeling.HQAlign：使用电流水平建模对齐纳米孔读取以进行 SV 检测。
Bioinformatics. 2023 Oct 3;39(10). doi: 10.1093/bioinformatics/btad580.
4
HQAlign: Aligning nanopore reads for SV detection using current-level modeling.HQAlign：使用电流水平建模对纳米孔读数进行比对以检测结构变异
bioRxiv. 2023 Jan 9:2023.01.08.523172. doi: 10.1101/2023.01.08.523172.
5
Theory of local k-mer selection with applications to long-read alignment.基于局部 k-mer 选择的理论及其在长读测序比对中的应用。
Bioinformatics. 2022 Oct 14;38(20):4659-4669. doi: 10.1093/bioinformatics/btab790.
6
Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining.使用 minimap2-fpga 与硬件加速链接集成实现高效的端到端长读序列映射。
Sci Rep. 2023 Nov 17;13(1):20174. doi: 10.1038/s41598-023-47354-8.
7
IMOS: improved Meta-aligner and Minimap2 On Spark.IMOS：改进的基于 Spark 的 Meta-aligner 和 Minimap2
BMC Bioinformatics. 2019 Jan 24;20(1):51. doi: 10.1186/s12859-018-2592-5.
8
Accurate spliced alignment of long RNA sequencing reads.长 RNA 测序reads 的精确拼接比对。
Bioinformatics. 2021 Dec 11;37(24):4643-4651. doi: 10.1093/bioinformatics/btab540.
9
HQAlign: Aligning nanopore reads for SV detection using current-level modeling.HQAlign：使用电流水平建模对纳米孔读数进行比对以检测结构变异
ArXiv. 2023 Jan 10:arXiv:2301.03834v1.
10
MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data.MinimapR：一种用于分析大规模第三代测序数据的并行比对工具。
Comput Biol Chem. 2022 Aug;99:107735. doi: 10.1016/j.compbiolchem.2022.107735. Epub 2022 Jul 13.
引用本文的文献
1
A Prelude to Conservation Genomics: First Chromosome-Level Genome Assembly of a Flying Squirrel (Pteromyini: ).保护基因组学的前奏：飞鼠（鼯鼠族：）的首个染色体水平基因组组装
Ecol Evol. 2025 Sep 1;15(9):e71905. doi: 10.1002/ece3.71905. eCollection 2025 Sep.
2
EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis.EASYstrata：用于基因组注释和基因组差异分析的一体化工作流程。
NAR Genom Bioinform. 2025 Aug 27;7(3):lqaf110. doi: 10.1093/nargab/lqaf110. eCollection 2025 Sep.
3
Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs.通过直肠拭子的长读长宏基因组下一代测序对碳青霉烯类耐药肠杆菌科细菌定植患者的微生物组和耐药组特征进行分析。
JAC Antimicrob Resist. 2025 Aug 28;7(4):dlaf152. doi: 10.1093/jacamr/dlaf152. eCollection 2025 Aug.
4
Long-read sequencing identifies ATXN3 repeat expansions, and transcriptomics reveals disease progression biomarkers and druggable targets for spinocerebellar ataxia type 3.长读长测序可识别ATXN3重复序列扩增，转录组学揭示了3型脊髓小脑共济失调的疾病进展生物标志物和可成药靶点。
BMC Neurol. 2025 Sep 1;25(1):370. doi: 10.1186/s12883-025-04378-z.
5
Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner.通过使用TranSigner准确分配长RNA测序读数来增强转录组表达定量。
Genome Biol. 2025 Aug 28;26(1):257. doi: 10.1186/s13059-025-03723-2.
6
Genetic basis for broad interspecific compatibility in Solanum verrucosum.马铃薯疣粒种广泛种间兼容性的遗传基础。
Plant J. 2025 Aug;123(4):e70426. doi: 10.1111/tpj.70426.
7
Evolutionary Consequences of Unusually Large Pericentric TE-rich Regions in the Genome of a Neotropical Fig Wasp.新热带区榕小蜂基因组中异常大的富含着丝粒转座元件区域的进化后果
Genome Biol Evol. 2025 Sep 2;17(9). doi: 10.1093/gbe/evaf158.
8
Experimental evidence of vaccine-driven evolution of respiratory syndrome virus type 2.2型呼吸道综合征病毒疫苗驱动进化的实验证据。
Virus Evol. 2025 Jul 22;11(1):veaf056. doi: 10.1093/ve/veaf056. eCollection 2025.
9
Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.全球泛基因组分析凸显结构变异在牛改良中的关键作用，并鉴定出一个独特事件作为IGFBP7 +细胞中的新型增强子。
Mol Biol Evol. 2025 Sep 1;42(9). doi: 10.1093/molbev/msaf205.
10
The pUL47 tegument protein of Marek's Disease Virus interacts with p32/C1QBP to promote horizontal transmission.马立克氏病病毒的pUL47被膜蛋白与p32/C1QBP相互作用以促进水平传播。
PLoS Pathog. 2025 Aug 19;21(8):e1013434. doi: 10.1371/journal.ppat.1013434. eCollection 2025 Aug.
Zotero 插件