kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on the K-Mer Neighborhood Graph

Wei, Ze-Gang; Fan, Xing-Guo; Zhang, Hao; Zhang, Xiaodan; Liu, Fei; Qian, Yu; Zhang, Shaowu

doi:10.3389/fgene.2022.890651

Cited by 6 publications

(8 citation statements)

References 45 publications

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Section: Anchor Chaining Using Longest Subsequences Of Anchorsmentioning

confidence: 99%

“…Note that other methods use graphs built over anchors as backbones to the chaining and alignment steps without fuzzy seeds [73,49].…”

Section: Figure S2mentioning

confidence: 99%

“…While this survey covers the genomic mapping aspects, other important contributions have dealt with adapted procedures in the case of long-read RNA mapping [54, 66, 51, 75], and structural variant identification [69, 49, 25, 74], or other specialized problems [56]. Other related research focused on read-to-read overlap detection [20, 76] 2 , or alignment-free/pseudo-mapping approaches [34, 13].…”

Section: Definitions and State-of-the-art Of Toolsmentioning

confidence: 99%

“…They are complemented with heuristics or replaced by more recent approaches in Section 3.3.3. In addition, several methods use graphs built over anchors as backbones to the chaining and alignment steps [74, 50, 72] (one approach is described in the Appendix). Because they would fail to take into account distances between anchors, these methods have been replaced by dynamic programming approaches relying on gap score functions.…”

Section: A Survey Of Algorithmic Stepsmentioning

confidence: 99%

“…After the LCSk pass, a L1 linear regression step is applied to fit a straight line with a 45 degree slope and remove outliers, especially in the beginning and end of the chain (see case 4 in Figure 4 in the main text). Note that other methods use graphs built over anchors as backbones to the chaining and alignment steps without fuzzy seeds [74, 50].

Figure S2 Query in Graphmap, different possible sequences can be matched using a single key.…”

Section: Graphmap’s Indexing Strategy For Fuzzy Seedsmentioning

confidence: 99%

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A survey of mapping algorithms in the long-reads era

Sahlin

Baudeau

Cazaux

et al. 2022

Preprint

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It has been ten years since the first publication of a method dedicated entirely to mapping third-generation sequencing long-reads. The unprecedented characteristics of this new type of sequencing data created a shift, and methods moved on from the seed-and-extend framework previously used for short reads to a seed-and-chain framework due to the abundance of seeds in each read. As a result, the main novelties in proposed long-read mapping algorithms are typically based on alternative seed constructs or chaining formulations. Dozens of tools now exist, whose heuristics have considerably evolved with time. The rapid progress of the field, synchronized with the frequent improvements of data, does not make the literature and implementations easy to keep up with. Therefore, in this survey article, we provide an overview of existing mapping methods for long reads with insights into algorithmic details.

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Section: Anchor Chaining Using Longest Subsequences Of Anchorsmentioning

confidence: 99%

“…Note that other methods use graphs built over anchors as backbones to the chaining and alignment steps without fuzzy seeds [73,49].…”

Section: Figure S2mentioning

confidence: 99%

Section: Definitions and State-of-the-art Of Toolsmentioning

confidence: 99%

Section: A Survey Of Algorithmic Stepsmentioning

confidence: 99%

Figure S2 Query in Graphmap, different possible sequences can be matched using a single key.…”

Section: Graphmap’s Indexing Strategy For Fuzzy Seedsmentioning

confidence: 99%

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A survey of mapping algorithms in the long-reads era

Sahlin

Baudeau

Cazaux

et al. 2022

Preprint

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Bioinformatics for Plant Genetics and Breeding Research

Naik,

Zhao,

Channale

et al. 2024

Sustainability Sciences in Asia and Africa

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Global food demand is expected to increase between 55 and 70% by 2050. Plant breeders and geneticists are constantly under pressure to develop highyielding climate-resilient varieties using novel approaches. The quest for simplifying complex traits and efforts for developing high-yielding varieties during the twentyfirst century led to a paradigm shift from phenotypic-based selection to genomebased breeding. On one hand, the development and utilization of diverse genetic

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pathMap: a path-based mapping tool for long noisy reads with high sensitivity

Wei,

Zhang,

Fan

et al. 2024

Briefings in Bioinformatics

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With the rapid development of single-molecule sequencing (SMS) technologies, the output read length is continuously increasing. Mapping such reads onto a reference genome is one of the most fundamental tasks in sequence analysis. Mapping sensitivity is becoming a major concern since high sensitivity can detect more aligned regions on the reference and obtain more aligned bases, which are useful for downstream analysis. In this study, we present pathMap, a novel k-mer graph-based mapper that is specifically designed for mapping SMS reads with high sensitivity. By viewing the alignment chain as a path containing as many anchors as possible in the matched k-mer graph, pathMap treats chaining as a path selection problem in the directed graph. pathMap iteratively searches the longest path in the remaining nodes; more candidate chains with high quality can be effectively detected and aligned. Compared to other state-of-the-art mapping methods such as minimap2 and Winnowmap2, experiment results on simulated and real-life datasets demonstrate that pathMap obtains the number of mapped chains at least 11.50% more than its closest competitor and increases the mapping sensitivity by 17.28% and 13.84% of bases over the next-best mapper for Pacific Biosciences and Oxford Nanopore sequencing data, respectively. In addition, pathMap is more robust to sequence errors and more sensitive to species- and strain-specific identification of pathogens using MinION reads.

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kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on the K-Mer Neighborhood Graph

Cited by 6 publications

References 45 publications

A survey of mapping algorithms in the long-reads era

A survey of mapping algorithms in the long-reads era

Bioinformatics for Plant Genetics and Breeding Research

pathMap: a path-based mapping tool for long noisy reads with high sensitivity

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