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| Format: | Preprint |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2409.05214 |
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| _version_ | 1866910597267849216 |
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| author | Marchet, Camille |
| author_facet | Marchet, Camille |
| contents | This paper provides a comprehensive review of recent advancements in k-mer-based data structures representing collections of several samples (sometimes called colored de Bruijn graphs) and their applications in large-scale sequence indexing and pangenomics. The review explores the evolution of k-mer set representations, highlighting the trade-offs between exact and inexact methods, as well as the integration of compression strategies and modular implementations. I discuss the impact of these structures on practical applications and describe recent utilization of these methods for analysis. By surveying the state-of-the-art techniques and identifying emerging trends, this work aims to guide researchers in selecting and developing methods for large scale and reference-free genomic data. For a broader overview of k-mer set representations and foundational data structures, see the accompanying article on practical k-mer sets. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_05214 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Advances in colored k-mer sets: essentials for the curious Marchet, Camille Genomics This paper provides a comprehensive review of recent advancements in k-mer-based data structures representing collections of several samples (sometimes called colored de Bruijn graphs) and their applications in large-scale sequence indexing and pangenomics. The review explores the evolution of k-mer set representations, highlighting the trade-offs between exact and inexact methods, as well as the integration of compression strategies and modular implementations. I discuss the impact of these structures on practical applications and describe recent utilization of these methods for analysis. By surveying the state-of-the-art techniques and identifying emerging trends, this work aims to guide researchers in selecting and developing methods for large scale and reference-free genomic data. For a broader overview of k-mer set representations and foundational data structures, see the accompanying article on practical k-mer sets. |
| title | Advances in colored k-mer sets: essentials for the curious |
| topic | Genomics |
| url | https://arxiv.org/abs/2409.05214 |