scholarly journals Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

2021 ◽  
Author(s):  
Zhenxian Zheng ◽  
Shumin Li ◽  
Junhao Su ◽  
Amy Wing-Sze Leung ◽  
Tak-Wah Lam ◽  
...  
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Variant Calling ◽  
The Other ◽  
Snp Calling ◽  
Long Reads ◽  
Pile Up ◽  
Long Read

Deep learning-based variant callers are becoming the standard and have achieved superior SNP calling performance using long reads. In this paper, we present Clair3, which makes the best of two major method categories: pile-up calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 ran faster than any of the other state-of-the-art variant callers and performed the best, especially at lower coverage.

scholarly journals Dysgu: efficient structural variant calling using short or long reads

2021 ◽  
Author(s):  
Duncan M Baird ◽  
Kez Cleal
Keyword(s):  
Structural Variation ◽  
State Of The Art ◽  
Variant Calling ◽  
High Sensitivity ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Long Read ◽  
Low Coverage ◽  
Paired End Sequencing

Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), although paired-end sequencing offers better scalability. Here, we present dysgu, which calls SVs or indels using paired-end or long reads. Dysgu detects signals from alignment gaps, discordant and supplementary mappings, and generates consensus contigs, before classifying events using machine learning. Additional SVs are identified by remapping of anomalous sequences. Dysgu outperforms existing state-of-the-art tools using paired-end or long-reads, offering high sensitivity and precision whilst being among the fastest tools to run. We find that combining low coverage paired-end and long-reads is competitive in terms of performance with long-reads at higher coverage values.

scholarly journals Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap

2015 ◽  
Author(s):  
Ivan Sovic ◽  
Mile Sikic ◽  
Andreas Wilm ◽  
Shannon Nicole Fenlon ◽  
Swaine Chen ◽  
...  
Keyword(s):  
Human Genome ◽  
Variant Calling ◽  
Error Rates ◽  
Nanopore Sequencing ◽  
Structural Variants ◽  
Specific Identification ◽  
Long Reads ◽  
Long Read ◽  
Specific Error ◽  
Very High

Exploiting the power of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. We present the first nanopore read mapper (GraphMap) that uses a read-funneling paradigm to robustly handle variable error rates and fast graph traversal to align long reads with speed and very high precision (>95%). Evaluation on MinION sequencing datasets against short and long-read mappers indicates that GraphMap increases mapping sensitivity by at least 15-80%. GraphMap alignments are the first to demonstrate consensus calling with <1 error in 100,000 bases, variant calling on the human genome with 76% improvement in sensitivity over the next best mapper (BWA-MEM), precise detection of structural variants from 100bp to 4kbp in length and species and strain-specific identification of pathogens using MinION reads. GraphMap is available open source under the MIT license at https://github.com/isovic/graphmap.

scholarly journals Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru

2020 ◽  
Author(s):  
Andrew J. Page ◽  
Nabil-Fareed Alikhan ◽  
Michael Strinden ◽  
Thanh Le Viet ◽  
Timofey Skvortsov
Keyword(s):  
Mycobacterium Tuberculosis ◽  
State Of The Art ◽  
Sequence Data ◽  
Human Pathogen ◽  
Sequencing Data ◽  
Short Read ◽  
Short Read Sequencing ◽  
Long Reads ◽  
Long Read

AbstractSpoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected long read. It allows for near real-time spoligotyping from long read data as it is being sequenced, giving rapid sample typing. We compare it to the existing state of the art software and find it performs identically to the results obtained from short read sequencing data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru under the GPLv3 open source licence.

Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Data Science ◽  
State Of The Art ◽  
Hybrid Models ◽  
The Other ◽  
Learning Models ◽  
Comprehensive Review

Abstract This paper provides the state of the art of data science in economics. Through a novel taxonomy of applications and methods advances in data science are investigated. The data science advances are investigated in three individual classes of deep learning models, ensemble models, and hybrid models. Application domains include stock market, marketing, E-commerce, corporate banking, and cryptocurrency. Prisma method, a systematic literature review methodology is used to ensure the quality of the survey. The findings revealed that the trends are on advancement of hybrid models as more than 51% of the reviewed articles applied hybrid model. On the other hand, it is found that based on the RMSE accuracy metric, hybrid models had higher prediction accuracy than other algorithms. While it is expected the trends go toward the advancements of deep learning models.

scholarly journals Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Davide Bolognini ◽  
Alberto Magi
Keyword(s):  
Variant Calling ◽  
Research Report ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Factors Affecting ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Sequencing Studies ◽  
Long Read

Structural variants (SVs) are genomic rearrangements that involve at least 50 nucleotides and are known to have a serious impact on human health. While prior short-read sequencing technologies have often proved inadequate for a comprehensive assessment of structural variation, more recent long reads from Oxford Nanopore Technologies have already been proven invaluable for the discovery of large SVs and hold the potential to facilitate the resolution of the full SV spectrum. With many long-read sequencing studies to follow, it is crucial to assess factors affecting current SV calling pipelines for nanopore sequencing data. In this brief research report, we evaluate and compare the performances of five long-read SV callers across four long-read aligners using both real and synthetic nanopore datasets. In particular, we focus on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs of different types and size ranges and provide insights into precision and recall of SV callsets generated by integrating the various long-read aligners and SV callers. The computational pipeline we propose is publicly available at https://github.com/davidebolo1993/EViNCe and can be adjusted to further evaluate future nanopore sequencing datasets.

scholarly journals NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks

2019 ◽  
Author(s):  
Umair Ahsan ◽  
Qian Liu ◽  
Li Fang ◽  
Kai Wang
Keyword(s):  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Variant Calling ◽  
Sequencing Data ◽  
Long Reads ◽  
Novel Variants ◽  
Long Read ◽  
Variant Detection ◽  
Genomic Regions ◽  
Haplotype Information

AbstractVariant (SNPs/indels) detection from high-throughput sequencing data remains an important yet unresolved problem. Long-read sequencing enables variant detection in difficult-to-map genomic regions that short-read sequencing cannot reliably examine (for example, only ~80% of genomic regions are marked as “high-confidence region” to have SNP/indel calls in the Genome In A Bottle project); however, the high per-base error rate poses unique challenges in variant detection. Existing methods on long-read data typically rely on analyzing pileup information from neighboring bases surrounding a candidate variant, similar to short-read variant callers, yet the benefits of much longer read length are not fully exploited. Here we present a deep neural network called NanoCaller, which detects SNPs by examining pileup information solely from other nonadjacent candidate SNPs that share the same long reads using long-range haplotype information. With called SNPs by NanoCaller, NanoCaller phases long reads and performs local realignment on two sets of phased reads to call indels by another deep neural network. Extensive evaluation on 5 human genomes (sequenced by Nanopore and PacBio long-read techniques) demonstrated that NanoCaller greatly improved performance in difficult-to-map regions, compared to other long-read variant callers. We experimentally validated 41 novel variants in difficult-to-map regions in a widely-used benchmarking genome, which cannot be reliably detected previously. We extensively evaluated the run-time characteristics and the sensitivity of parameter settings of NanoCaller to different characteristics of sequencing data. Finally, we achieved the best performance in Nanopore-based variant calling from MHC regions in the PrecisionFDA Variant Calling Challenge on Difficult-to-Map Regions by ensemble calling. In summary, by incorporating haplotype information in deep neural networks, NanoCaller facilitates the discovery of novel variants in complex genomic regions from long-read sequencing data.

scholarly journals LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

2021 ◽  
Author(s):  
Jyun-Hong Lin ◽  
Liang-Chi Chen ◽  
Shu-Qi Yu ◽  
Yao-Ting Huang
Keyword(s):  
Variant Calling ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Chromosome Conformation ◽  
Long Reads ◽  
Cost Effective Approach ◽  
Long Read ◽  
Microbial Strains

AbstractLong-read phasing has been used for reconstructing diploid genomes, improving variant calling, and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), and the efficiency is unsatisfactory for population-scale phasing. This paper presents an ultra-fast algorithm, LongPhase, which can simultaneously phase single nucleotide polymorphisms (SNPs) and SVs of a human genome in ∼10-20 minutes, 10x faster than the state-of-the-art WhatsHap and Margin. In particular, LongPhase produces much larger phased blocks at almost chromosome level with only long reads (N50=26Mbp). We demonstrate that LongPhase combined with Nanopore is a cost-effective approach for providing chromosome-scale phasing without the need for additional trios, chromosome-conformation, and single-cell strand-seq data.

scholarly journals Data Science in Economics: Comprehensive Review of Advanced Machine Learning and Deep Learning Methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Data Science ◽  
State Of The Art ◽  
Hybrid Models ◽  
The Other ◽  
Learning Models ◽  
Comprehensive Review

This paper provides the state of the art of data science in economics. Through a novel taxonomy of applications and methods advances in data science are investigated. The data science advances are investigated in three individual classes of deep learning models, ensemble models, and hybrid models. Application domains include stock market, marketing, E-commerce, corporate banking, and cryptocurrency. Prisma method, a systematic literature review methodology is used to ensure the quality of the survey. The findings revealed that the trends are on advancement of hybrid models as more than 51% of the reviewed articles applied hybrid model. On the other hand, it is found that based on the RMSE accuracy metric, hybrid models had higher prediction accuracy than other algorithms. While it is expected the trends go toward the advancements of deep learning models.

scholarly journals AsmMix: A pipeline for high quality diploid de novo assembly

2021 ◽  
Author(s):  
Pei Wu ◽  
Chao Liu ◽  
Ou Wang ◽  
Xia Zhao ◽  
Fang Chen ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Variant Calling ◽  
The Other ◽  
Second Step ◽  
Small Scale ◽  
Mixing Process ◽  
High Quality ◽  
Single Molecule Sequencing ◽  
Long Read

AbstractIn this paper, we report a pipeline, AsmMix, which is capable of producing both contiguous and high-quality diploid genomes. The pipeline consists of two steps. In the first step, two sets of assemblies are generated: one is based on co-barcoded reads, which are highly accurate and haplotype-resolved but contain many gaps, the other assembly is based on single-molecule sequencing reads, which is contiguous but error-prone. In the second step, those two sets of assemblies are compared and integrated into a haplotype-resolved assembly with fewer errors. We test our pipeline using a dataset of human genome NA24385, perform variant calling from those assemblies and then compare against GIAB Benchmark. We show that AsmMix pipeline could produce highly contiguous, accurate, and haplotype-resolved assemblies. Especially the assembly mixing process could effectively reduce small-scale errors in the long read assembly.

scholarly journals cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs

2019 ◽  
Vol 35 (14) ◽  
pp. i61-i70 ◽  
Author(s):  
Ivan Tolstoganov ◽  
Anton Bankevich ◽  
Zhoutao Chen ◽  
Pavel A Pevzner
Keyword(s):  
Narrow Range ◽  
State Of The Art ◽  
Supplementary Information ◽  
De Bruijn Graph ◽  
Hybrid Assembly ◽  
De Bruijn Graphs ◽  
Long Reads ◽  
Long Read ◽  
De Bruijn ◽  
New Applications

Abstract Motivation The recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly. Results We describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed. Availability and implementation Source code and installation manual for cloudSPAdes are available at https://github.com/ablab/spades/releases/tag/cloudspades-paper. Supplementary Information Supplementary data are available at Bioinformatics online.

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