Anchorage accurately assembles anchor-flanked synthetic long reads
Abstract Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
|
| Series: | Algorithms for Molecular Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13015-025-00288-4 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849333770166992896 |
|---|---|
| author | Xiaofei Carl Zang Xiang Li Kyle Metcalfe Tuval Ben-Yehezkel Ryan Kelley Mingfu Shao |
| author_facet | Xiaofei Carl Zang Xiang Li Kyle Metcalfe Tuval Ben-Yehezkel Ryan Kelley Mingfu Shao |
| author_sort | Xiaofei Carl Zang |
| collection | DOAJ |
| description | Abstract Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol. LoopSeq Solo also achieves ultra-high sequencing depth and high purity of short reads covering the entire captured molecule. Despite the availability of many assembly methods, constructing full-length sequence from these anchor-enabled, ultra-high coverage sequencing data remains challenging due to the complexity of the underlying assembly graphs and the lack of specific algorithms leveraging anchors. We present Anchorage, a novel assembler that performs anchor-guided assembly for ultra-high-depth sequencing data. Anchorage starts with a kmer-based approach for precise estimation of molecule lengths. It then formulates the assembly problem as finding an optimal path that connects the two nodes determined by anchors in the underlying compact de Bruijn graph. The optimality is defined as maximizing the weight of the smallest node while matching the estimated sequence length. Anchorage uses a modified dynamic programming algorithm to efficiently find the optimal path. Through both simulations and real data, we show that Anchorage outperforms existing assembly methods, particularly in the presence of sequencing artifacts. Anchorage fills the gap in assembling anchor-enabled data. We anticipate its broad use as anchor-enabled sequencing technologies become prevalent. Anchorage is freely available at https://github.com/Shao-Group/anchorage ; the scripts and documents that can reproduce all experiments in this manuscript are available at https://github.com/Shao-Group/anchorage-test . |
| format | Article |
| id | doaj-art-4035aafaa9c04ed49d01802b16b9d236 |
| institution | Kabale University |
| issn | 1748-7188 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj-art-4035aafaa9c04ed49d01802b16b9d2362025-08-20T03:45:45ZengBMCAlgorithms for Molecular Biology1748-71882025-07-0120111610.1186/s13015-025-00288-4Anchorage accurately assembles anchor-flanked synthetic long readsXiaofei Carl Zang0Xiang Li1Kyle Metcalfe2Tuval Ben-Yehezkel3Ryan Kelley4Mingfu Shao5Huck Institutes of the Life Sciences, The Pennsylvania State UniversityDepartment of Computer Science and Engineering, The Pennsylvania State UniversityElement BiosciencesElement BiosciencesElement BiosciencesHuck Institutes of the Life Sciences, The Pennsylvania State UniversityAbstract Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol. LoopSeq Solo also achieves ultra-high sequencing depth and high purity of short reads covering the entire captured molecule. Despite the availability of many assembly methods, constructing full-length sequence from these anchor-enabled, ultra-high coverage sequencing data remains challenging due to the complexity of the underlying assembly graphs and the lack of specific algorithms leveraging anchors. We present Anchorage, a novel assembler that performs anchor-guided assembly for ultra-high-depth sequencing data. Anchorage starts with a kmer-based approach for precise estimation of molecule lengths. It then formulates the assembly problem as finding an optimal path that connects the two nodes determined by anchors in the underlying compact de Bruijn graph. The optimality is defined as maximizing the weight of the smallest node while matching the estimated sequence length. Anchorage uses a modified dynamic programming algorithm to efficiently find the optimal path. Through both simulations and real data, we show that Anchorage outperforms existing assembly methods, particularly in the presence of sequencing artifacts. Anchorage fills the gap in assembling anchor-enabled data. We anticipate its broad use as anchor-enabled sequencing technologies become prevalent. Anchorage is freely available at https://github.com/Shao-Group/anchorage ; the scripts and documents that can reproduce all experiments in this manuscript are available at https://github.com/Shao-Group/anchorage-test .https://doi.org/10.1186/s13015-025-00288-4Genome assemblyDe Bruijn graphSynthetic long readsAnchor-guided assemblyLoopSeq |
| spellingShingle | Xiaofei Carl Zang Xiang Li Kyle Metcalfe Tuval Ben-Yehezkel Ryan Kelley Mingfu Shao Anchorage accurately assembles anchor-flanked synthetic long reads Algorithms for Molecular Biology Genome assembly De Bruijn graph Synthetic long reads Anchor-guided assembly LoopSeq |
| title | Anchorage accurately assembles anchor-flanked synthetic long reads |
| title_full | Anchorage accurately assembles anchor-flanked synthetic long reads |
| title_fullStr | Anchorage accurately assembles anchor-flanked synthetic long reads |
| title_full_unstemmed | Anchorage accurately assembles anchor-flanked synthetic long reads |
| title_short | Anchorage accurately assembles anchor-flanked synthetic long reads |
| title_sort | anchorage accurately assembles anchor flanked synthetic long reads |
| topic | Genome assembly De Bruijn graph Synthetic long reads Anchor-guided assembly LoopSeq |
| url | https://doi.org/10.1186/s13015-025-00288-4 |
| work_keys_str_mv | AT xiaofeicarlzang anchorageaccuratelyassemblesanchorflankedsyntheticlongreads AT xiangli anchorageaccuratelyassemblesanchorflankedsyntheticlongreads AT kylemetcalfe anchorageaccuratelyassemblesanchorflankedsyntheticlongreads AT tuvalbenyehezkel anchorageaccuratelyassemblesanchorflankedsyntheticlongreads AT ryankelley anchorageaccuratelyassemblesanchorflankedsyntheticlongreads AT mingfushao anchorageaccuratelyassemblesanchorflankedsyntheticlongreads |