bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/374868

LRScaf: Improving Draft Genomes Using Long Noisy Reads

Qin, M.·Wu, S.·Li, A.·Zhao, F.·Feng, H.·Ding, L.·Chang, Y.·Ruan, J.
View original source ↗Export metadata ↓

Abstract

BackgroundThe advent of Third Generation Sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promised to enhance the quality of fragmental draft assemblies constructed from Next Generation Sequencing (NGS) technologies. To date, a few of algorithms, i.e., SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS, have been released that are capable of improving draft assemblies. However, hybrid assembly on large genomes is still challenging.\n\nResultsWe develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf), that is capable of boosting assembly contiguity to a large extent using long reads. In our experiment, our method significantly improves the contiguity of human draft assemblies, increasing the NG50 value of CHM1 from 127.5 Kb to 10.4 Mb using 20-fold coverage PacBio dataset and the NG50 value of NA12878 from 115.7 Kb to 17.4 Mb using 35-fold coverage Nanopore dataset. The run time for the scaffolding procedure using LRScaf is the shortest in all cases of our experiment. Compared with the run time of SSPACE-LongRead, LRScaf is faster 300 times for S. cerevisiae and 2,300 times for D. melanogaster. The peak RAM of LRScaf, by contrast, is more efficient than LINKS in our test. For the rice case, the peak RAM of LINKS (877.72 Gb) is about 196 times higher than LRScaf. For the experiment of human assembly, the peak RAM of LINKS is beyond the capacity of system memory (1 Tb) whereas LRScaf takes 20.28 and 41.20 Gb on CHM1 and NA12878 datasets.\n\nConclusionsThe new method, LRScaf, yields the best or at least moderate contiguity and accuracy of scaffolds in the shortest run time compared with the state-of-the-art methods. Furthermore, it offers a new opportunity for the hybrid assembly of large genomes.

Source connections

Explore related subjects

bioinformaticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Qin, M., Wu, S., Li, A., Zhao, F., Feng, H., Ding, L., Chang, Y., Ruan, J.. 2018-07-24. LRScaf: Improving Draft Genomes Using Long Noisy Reads. https://doi.org/10.1101/374868

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression

Background: Improving crop adaptation and enhancing agronomic and quality traits requires a deeper understanding of gene expression regulation, for which expression atlases are valuable tools. Almond (Prunus dulcis (Mill.) D.A. Webb) is one of the most economically important tree nut crops worldwide. However, an integrated transcriptomic resource for this species is still lacking. Available data remain fragmented across independent studies, limiting their comparability and reuse. Results: Here, we present the first almond gene expression atlas: a comprehensive multi-tissue transcriptomic resource integrating publicly available RNA sequencing data. A total of 142 high-quality untreated and control samples from 17 independent projects were curated through a metadata standardization process and analyzed using a unified bioinformatics pipeline. Standardized expression profiles were generated for 25,225 annotated genes in the Prunus dulcis Texas v2.0 reference genome. The atlas integrates two complementary expression approaches: a median TPM approach capturing quantitative expression levels and a rank-based strategy implemented using the Bgee expression calling method, designed to improve comparability across heterogeneous datasets. This design enables the identification of tissue-specific candidate genes and the exploration of expression patterns across tissues and developmental stages. Its applicability is demonstrated through two use cases, highlighting its ability to identify biologically meaningful gene sets associated with bud dormancy transitions and to prioritize candidate reference genes for RT-qPCR normalization in almond. Conclusions: The Almond Expression Atlas v1.0 is publicly available through FruitDBase (fruitdbase.csic.es), providing an interactive platform for gene expression exploration and visualization. This resource supports functional genomics studies and facilitates candidate gene discovery in almond, while ensuring data traceability and promoting data reusability.

bioinformatics↗
bioRxiv2026

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

Single amino acid mutations are among the most common forms of genetic variation, with effects ranging from negligible to severe disruption of protein function. Accurate quantitative evaluation of protein variants therefore represents a key challenge in medicine and protein engineering. Computational variant effect predictors (VEPs) are widely used to prioritize missense variants, yet their fair comparison is hindered by data circularity, benchmarks restricted to human clinical annotations, and limited availability of code and training data, all of which can inflate apparent performance. Here, we reviewed 18 recent and 3 older, widely adopted variant effect predictors for reproducible benchmarking and assembled a rigorously curated, leakage-controlled Benchmark dataset by integrating clinically annotated human variants from ClinVar and Humsavar as well as cross-species variants with functional annotations. The evaluation on this dataset revealed a narrow overall performance range for the benchmarked tools (AUC 0.631-0.758) and a consistent drop from clinical to functional data. Surprisingly, several tools published two decades ago demonstrated comparable performance to mid-ranked modern predictors. Building on these results, we developed a gradient-boosting consensus model, PredictSNPprot, which achieved an AUC of 0.82 on a held-out test set, outperforming the original PredictSNP meta-predictor and the best individual state-of-the-art tool by 13.6 and 5.7 percentage points, respectively. The Benchmark dataset, including the predictions from the evaluated tools, is available at https://doi.org/10.5281/zenodo.23597130 and PredictSNPprot consensus predictor is available at https://github.com/loschmidt/PredictSNPprot.

bioinformatics↗
bioRxiv2026

MaCADEMIA: a software toolbox for single-molecule fluorescence image quantification

Single-molecule localisation microscopy (SMLM) is a powerful tool in molecular and cellular biology and part of the broad umbrella of super-resolution microscopy. A distinct feature of SMLM, is its capacity for deep quantification, beyond just spatial information, to copy number, stoichiometry, molecular interaction and dynamics in living cells. The hardware required is increasingly straightforward to implement. However, complexity remains in the image analysis where much remains fragmented across specialised software tools. Here, we present MaCADEMIA (Matlab Computational Analysis of Diffusion, Emitter Molecular Intensity and Abundance), a simple yet powerful toolbox of MATLAB functions and associated documentation to enable straightforward extraction of quantitative single-molecule information. MaCADEMIA performs ensemble particle detection achieving localisation accuracies down to 0.5 pixels Root mean squared error (RMSE) across wide signal-to-noise (SNR) ranges on standardised particle tracking benchmarks, consistently matching or exceeding the performance of 14 leading methods. Our integrated workflow enables molecular counting and stoichiometry determination through stepwise photobleaching analysis, mobility measurement via mean squared displacement, colocalisaton analysis and absolute protein copy number quantification using three-dimensional cellular models.

bioinformatics↗