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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Li D, Liu CM, Luo R, Sadakane K, Lam TW. Li D, et al. Bioinformatics. 2015 May 15;31(10):1674-6. doi: 10.1093/bioinformatics/btv033. Epub 2015 Jan 20. Bioinformatics. 2015. PMID: 25609793 Free article.
MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing …
MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finish …
Meta-colored compacted de Bruijn graphs.
Pibiri GE, Fan J, Patro R. Pibiri GE, et al. bioRxiv [Preprint]. 2023 Nov 1:2023.07.21.550101. doi: 10.1101/2023.07.21.550101. bioRxiv. 2023. PMID: 37546988 Free PMC article. Preprint.
MOTIVATION: The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. ...Reducing the space of the colors is therefore of utmost importance for large-scale sequence indexing. RESULTS: We descri …
MOTIVATION: The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics …
Succinct dynamic de Bruijn graphs.
Alipanahi B, Kuhnle A, Puglisi SJ, Salmela L, Boucher C. Alipanahi B, et al. Bioinformatics. 2021 Aug 4;37(14):1946-1952. doi: 10.1093/bioinformatics/btaa546. Bioinformatics. 2021. PMID: 32462192 Free PMC article.
MOTIVATION: The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. ...RESULTS: In this article, we present DynamicBOSS, a succinct representation of the de Bruijn graph that allows for an unlimite …
MOTIVATION: The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. ... …
On the Hardness of Sequence Alignment on De Bruijn Graphs.
Gibney D, Thankachan SV, Aluru S. Gibney D, et al. J Comput Biol. 2022 Dec;29(12):1377-1396. doi: 10.1089/cmb.2022.0411. Epub 2022 Nov 25. J Comput Biol. 2022. PMID: 36450127
Moreover, NP-completeness continues to hold even when edits are restricted to only substitutions. Despite the popularity of the de Bruijn graphs in Computational Biology, the complexity of approximate pattern matching on the de Bruijn graphs remained u …
Moreover, NP-completeness continues to hold even when edits are restricted to only substitutions. Despite the popularity of the de …
Lossless indexing with counting de Bruijn graphs.
Karasikov M, Mustafa H, Rätsch G, Kahles A. Karasikov M, et al. Genome Res. 2022 May 24;32(9):1754-64. doi: 10.1101/gr.276607.122. Online ahead of print. Genome Res. 2022. PMID: 35609994 Free PMC article.
In this work, we propose counting de Bruijn graphs, a notion generalizing annotated de Bruijn graphs by supplementing each node-label relation with one or many attributes (e.g., a k-mer count or its positions). Counting de Bruijn g …
In this work, we propose counting de Bruijn graphs, a notion generalizing annotated de Bruijn graphs by suppleme …
Triglyceride Lowering with Pemafibrate to Reduce Cardiovascular Risk.
Das Pradhan A, Glynn RJ, Fruchart JC, MacFadyen JG, Zaharris ES, Everett BM, Campbell SE, Oshima R, Amarenco P, Blom DJ, Brinton EA, Eckel RH, Elam MB, Felicio JS, Ginsberg HN, Goudev A, Ishibashi S, Joseph J, Kodama T, Koenig W, Leiter LA, Lorenzatti AJ, Mankovsky B, Marx N, Nordestgaard BG, Páll D, Ray KK, Santos RD, Soran H, Susekov A, Tendera M, Yokote K, Paynter NP, Buring JE, Libby P, Ridker PM; PROMINENT Investigators. Das Pradhan A, et al. N Engl J Med. 2022 Nov 24;387(21):1923-1934. doi: 10.1056/NEJMoa2210645. Epub 2022 Nov 5. N Engl J Med. 2022. PMID: 36342113 Clinical Trial.
MBG: Minimizer-based sparse de Bruijn Graph construction.
Rautiainen M, Marschall T. Rautiainen M, et al. Bioinformatics. 2021 Aug 25;37(16):2476-2478. doi: 10.1093/bioinformatics/btab004. Bioinformatics. 2021. PMID: 33475133 Free PMC article.
MOTIVATION: De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally, long-read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads ha …
MOTIVATION: De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditional …
deGSM: Memory Scalable Construction Of Large Scale de Bruijn Graph.
Guo H, Fu Y, Gao Y, Li J, Wang Y, Liu B. Guo H, et al. IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov-Dec;18(6):2157-2166. doi: 10.1109/TCBB.2019.2913932. Epub 2021 Dec 8. IEEE/ACM Trans Comput Biol Bioinform. 2021. PMID: 31056509
With the rapid development of HTS data and ever-increasing number of assembled genomes, there is a high demand to construct the very large de Bruijn graph for sequences up to Tera-base-pair level. Current approaches may have unaffordable memory footprints to handle …
With the rapid development of HTS data and ever-increasing number of assembled genomes, there is a high demand to construct the very large …
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.
Pandey P, Bender MA, Johnson R, Patro R. Pandey P, et al. Bioinformatics. 2017 Jul 15;33(14):i133-i141. doi: 10.1093/bioinformatics/btx261. Bioinformatics. 2017. PMID: 28881995 Free PMC article.
Because of the centrality of de Bruijn Graphs, researchers have proposed numerous methods for representing de Bruijn Graphs compactly. ...RESULTS: We present a method for compactly representing the weighted de Bruijn Graph (i.e. wi …
Because of the centrality of de Bruijn Graphs, researchers have proposed numerous methods for representing de Bruijn …
Superbubbles revisited.
Gärtner F, Müller L, Stadler PF. Gärtner F, et al. Algorithms Mol Biol. 2018 Dec 1;13:16. doi: 10.1186/s13015-018-0134-3. eCollection 2018. Algorithms Mol Biol. 2018. PMID: 30519278 Free PMC article.
123 results