Long-read single-molecule sequencing has revolutionized genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a rapid assembler, which, unlike contemporaneous SMS assemblers, does not require highly accurate raw reads for error correction. It has performed well in the evaluation of congeneric assemblers and has been successfully users for various assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015; here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632051 | PMC |
| http://dx.doi.org/10.46471/gigabyte.15 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
[Research progress and application of nanopores in single-molecule protein sensing].
Sheng Wu Gong Cheng Xue Bao
January 2025
School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing 210023, Jiangsu, China.
Proteins are fundamental carriers as the structural elements and biochemically active entities responsible for catalysis, transport, and regulation. These functions are depending on the protein folding into precise three-dimensional structures, interacting with ligands, and conformational changes. This article reviews the recent progress of nanopores in single-molecule protein sensing, involving the identification of polypeptides and proteins, the conformation changes of protein folding, the molecular structure responsible to the pH of solutions, the molecular interactions, and protein sequencing.
View Article and Find Full Text PDFThe Research Progress of Single-Molecule Sequencing and Its Significance in Nucleic Acid Metrology.
Biosensors (Basel)
December 2024
Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China.
Single-molecule sequencing technology, a novel method for gene sequencing, utilizes nano-sized materials to detect electrical and fluorescent signals. Compared to traditional Sanger sequencing and next-generation sequencing technologies, it offers significant advantages, including ultra-long read lengths, rapid sequencing, and the absence of amplification steps, making it widely applicable across various fields. By examining the development and components of single-molecule sequencing technology, it becomes clear that its unique characteristics provide new opportunities for advancing metrological traceability.
View Article and Find Full Text PDFAssessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues.
J Pathol
January 2025
The Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia.
Spatial transcriptomics (ST) offers enormous potential to decipher the biological and pathological heterogeneity in precious archival cancer tissues. Traditionally, these tissues have rarely been used and only examined at a low throughput, most commonly by histopathological staining. ST adds thousands of times as many molecular features to histopathological images, but critical technical issues and limitations require more assessment of how ST performs on fixed archival tissues.
View Article and Find Full Text PDFAn integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis.
Nucleic Acids Res
January 2025
Department of Microbiology, Icahn School of Medicine at Mount Sinai, NY, NY 10029, USA.
Human endogenous retroviruses (HERVs) occupy a large portion of the human genome. Most HERVs are transcriptionally silent, but they can be reactivated during pathological states such as viral infection and certain cancers. The HERV-K HML-2 clade includes elements that recently integrated have in the human germ line and often contain intact open reading frames that possibly support peptide and protein expression.
View Article and Find Full Text PDFSingle-molecule analysis of PARP1-G-quadruplex interaction.
bioRxiv
January 2025
Department of Biochemistry and Molecular Biology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, 52242, USA.
The human genome contains numerous repetitive nucleotide sequences that display a propensity to fold into non-canonical DNA structures including G-quadruplexes (G4s). G4s have both positive and negative impacts on various aspects of nucleic acid metabolism including DNA replication, DNA repair and RNA transcription. Poly (ADP-ribose) polymerase (PARP1), an important anticancer drug target, has been recently shown to bind a subset of G4s, and to undergo auto-PARylation.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!