SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies.

Structural variation (SV) is an important form of genomic variation that influences gene function and expression by altering the structure of the genome. Although long-read data have been proven to better characterize SVs, SVs detected from noisy long-read data still include a considerable portion of false-positive calls. To accurately detect SVs in long-read data, we present SVDF, a method that employs a learning-based noise filtering strategy and an SV signature-adaptive clustering algorithm, for effectively reducing the likelihood of false-positive events. Benchmarking results from multiple orthogonal experiments demonstrate that, across different sequencing platforms and depths, SVDF achieves higher calling accuracy for each sample compared to several existing general SV calling tools. We believe that, with its meticulous and sensitive SV detection capability, SVDF can bring new opportunities and advancements to cutting-edge genomic research.

INSnet: a method for detecting insertions based on deep learning network.

BACKGROUND: Many studies have shown that structural variations (SVs) strongly impact human disease. As a common type of SV, insertions are usually associated with genetic diseases. Therefore, accurately detecting insertions is of great significance. Although many methods for detecting insertions have been proposed, these methods often generate some errors and miss some variants. Hence, accurately detecting insertions remains a challenging task. RESULTS: In this paper, we propose a method named INSnet to detect insertions using a deep learning network. First, INSnet divides the reference genome into continuous sub-regions and takes five features for each locus through alignments between long reads and the reference genome. Next, INSnet uses a depthwise separable convolutional network. The convolution operation extracts informative features through spatial information and channel information. INSnet uses two attention mechanisms, the convolutional block attention module (CBAM) and efficient channel attention (ECA) to extract key alignment features in each sub-region. In order to capture the relationship between adjacent subregions, INSnet uses a gated recurrent unit (GRU) network to further extract more important SV signatures. After predicting whether a sub-region contains an insertion through the previous steps, INSnet determines the precise site and length of the insertion. The source code is available from GitHub at https://github.com/eioyuou/INSnet . CONCLUSION: Experimental results show that INSnet can achieve better performance than other methods in terms of F1 score on real datasets.

LcDel: deletion variation detection based on clustering and long reads.

Motivation: Genomic structural variation refers to chromosomal level variations such as genome rearrangement or insertion/deletion, which typically involve larger DNA fragments compared to single nucleotide variations. Deletion is a common type of structural variants in the genome, which may lead to mangy diseases, so the detection of deletions can help to gain insights into the pathogenesis of diseases and provide accurate information for disease diagnosis, treatment, and prevention. Many tools exist for deletion variant detection, but they are still inadequate in some aspects, and most of them ignore the presence of chimeric variants in clustering, resulting in less precise clustering results. Results: In this paper, we present LcDel, which can detect deletion variation based on clustering and long reads. LcDel first finds the candidate deletion sites and then performs the first clustering step using two clustering methods (sliding window-based and coverage-based, respectively) based on the length of the deletion. After that, LcDel immediately uses the second clustering by hierarchical clustering to determine the location and length of the deletion. LcDel is benchmarked against some other structural variation detection tools on multiple datasets, and the results show that LcDel has better detection performance for deletion. The source code is available in https://github.com/cyq1314woaini/LcDel.

LSnet: detecting and genotyping deletions using deep learning network.

The role and biological impact of structural variation (SV) are increasingly evident. Deletion accounts for 40% of SV and is an important type of SV. Therefore, it is of great significance to detect and genotype deletions. At present, high accurate long reads can be obtained as HiFi reads. And, through a combination of error-prone long reads and high accurate short reads, we can also get accurate long reads. These accurate long reads are helpful for detecting and genotyping SVs. However, due to the complexity of genome and alignment information, detecting and genotyping SVs remain a challenging task. Here, we propose LSnet, an approach for detecting and genotyping deletions with a deep learning network. Because of the ability of deep learning to learn complex features in labeled datasets, it is beneficial for detecting SV. First, LSnet divides the reference genome into continuous sub-regions. Based on the alignment between the sequencing data (the combination of error-prone long reads and short reads or HiFi reads) and the reference genome, LSnet extracts nine features for each sub-region, and these features are considered as signal of deletion. Second, LSnet uses a convolutional neural network and an attention mechanism to learn critical features in every sub-region. Next, in accordance with the relationship among the continuous sub-regions, LSnet uses a gated recurrent units (GRU) network to further extract more important deletion signatures. And a heuristic algorithm is present to determine the location and length of deletions. Experimental results show that LSnet outperforms other methods in terms of the F1 score. The source code is available from GitHub at https://github.com/eioyuou/LSnet.