Background Assembly guided by paper documents is the most widespread type used in the process of aircraft cable assembly.This process is very complicated and requires assembly workers with high-level skills.The techno...Background Assembly guided by paper documents is the most widespread type used in the process of aircraft cable assembly.This process is very complicated and requires assembly workers with high-level skills.The technologies of wearable Augmented Reality(AR)and portable visual inspection can be exploited to improve the efficiency and the quality of cable assembly.Methods In this study,we propose a smart assistance system for cable assembly that combines wearable AR with portable visual inspection.Specifically,a portable visual device based on binocular vision and deep learning is developed to realize fast detection and recognition of cable brackets that are installed on aircraft airframes.A Convolutional Neural Network(CNN)is then developed to read the texts on cables after images are acquired from the camera of the wearable AR device.An authoring tool that was developed to create and manage the assembly process is proposed to realize visual guidance of the cable assembly process based on a wearable AR device.The system is applied to cable assembly on an aircraft bulkhead prototype.Results The results show that this system can recognize the number,types,and locations of brackets,and can correctly read the text of aircraft cables.The authoring tool can assist users who lack professional programming experience in establishing a process plan,i.e.,assembly outline based on AR for cable assembly.Conclusions The system can provide quick assembly guidance for aircraft cable with texts,images,and a 3 D model.It is beneficial for reducing the dependency on paper documents,labor intensity,and the error rate.展开更多
The high-fidelity(HiFi)long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies.However,these assemblies still contain base-level errors,particularly within...The high-fidelity(HiFi)long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies.However,these assemblies still contain base-level errors,particularly within the error-prone regions of HiFi long reads.Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads.Here,we describe an upgraded genome polishing tool-NextPolish2,which can fix base errors remaining in those“highly accurate”genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors.We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere(T2T)genomes.NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.展开更多
Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequenc...Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequence.However,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence.Compared with traditional Sanger sequencing methods,although the throughput of NGS reads increases,the read length is shorter and the error rate is higher.It introduces several problems in assembling.Moreover,paired-end reads instead of single-end reads can be sampled which contain more information.The existing assemblers cannot fully utilize this information and fails to assemble longer contigs.In this article,we will revisit the major problems of assembling NGS reads on genomic,transcriptomic,metagenomic and metatranscriptomic data.We will also describe our IDBA package for solving these problems.IDBA package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth removal.Compared with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.展开更多
The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male...The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and Hi-C.We assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and YH2.0.By comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,respectively.In addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,respectively.Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.展开更多
Background:De novo genome assembly relies on two kinds of graphs:de Bruijn graphs and overlap graphs.Overlap graphs are the basis for the Celera assembler,while de Bruijn graphs have become the dominant technical devi...Background:De novo genome assembly relies on two kinds of graphs:de Bruijn graphs and overlap graphs.Overlap graphs are the basis for the Celera assembler,while de Bruijn graphs have become the dominant technical device in the last decade.Those two kinds of graphs are collectively called assembly graphs.Results:In this review,we discuss the most recent advances in the problem of constructing,representing and navigating assembly graphs,focusing on very large datasets.We will also explore some computational techniques,such as the Bloom filter,to compactly store graphs while keeping all functionalities intact.Conclusions:We complete our analysis with a discussion on the algorithmic issues of assembling from long reads(eg.,PacBio and Oxford Nanopore).Finally,we present some of the most relevant open problems in this field.展开更多
基金the Civil Airplane Technology Development Program(MJ-2017-G-70)Defense Industrial Technology Development Program(JCKY 2018601 C 011)the MIIT(Ministry of Industry and Information Technology)Key Laboratory of Smart Manufacturing for High-end Aerospace Products,and the Beijing Key Laboratory of Digital Design and Manufacturing.
文摘Background Assembly guided by paper documents is the most widespread type used in the process of aircraft cable assembly.This process is very complicated and requires assembly workers with high-level skills.The technologies of wearable Augmented Reality(AR)and portable visual inspection can be exploited to improve the efficiency and the quality of cable assembly.Methods In this study,we propose a smart assistance system for cable assembly that combines wearable AR with portable visual inspection.Specifically,a portable visual device based on binocular vision and deep learning is developed to realize fast detection and recognition of cable brackets that are installed on aircraft airframes.A Convolutional Neural Network(CNN)is then developed to read the texts on cables after images are acquired from the camera of the wearable AR device.An authoring tool that was developed to create and manage the assembly process is proposed to realize visual guidance of the cable assembly process based on a wearable AR device.The system is applied to cable assembly on an aircraft bulkhead prototype.Results The results show that this system can recognize the number,types,and locations of brackets,and can correctly read the text of aircraft cables.The authoring tool can assist users who lack professional programming experience in establishing a process plan,i.e.,assembly outline based on AR for cable assembly.Conclusions The system can provide quick assembly guidance for aircraft cable with texts,images,and a 3 D model.It is beneficial for reducing the dependency on paper documents,labor intensity,and the error rate.
基金supported by the National Key R&D Program of China(Grant No.2022YFC3400300)the National Natural Science Foundation of China(Grant Nos.32125009 and 32070663).
文摘The high-fidelity(HiFi)long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies.However,these assemblies still contain base-level errors,particularly within the error-prone regions of HiFi long reads.Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads.Here,we describe an upgraded genome polishing tool-NextPolish2,which can fix base errors remaining in those“highly accurate”genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors.We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere(T2T)genomes.NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.
基金supported in part by Hong Kong GRF HKU 7111/12E, 719611EShenzhen Basic Research Project JCYJ20120618143038947 (SIRI/04/04/2012/05)Outstanding Researcher Award (102009124).
文摘Sequence assembling is an important step for bioinformatics study.With the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular sequence.However,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence.Compared with traditional Sanger sequencing methods,although the throughput of NGS reads increases,the read length is shorter and the error rate is higher.It introduces several problems in assembling.Moreover,paired-end reads instead of single-end reads can be sampled which contain more information.The existing assemblers cannot fully utilize this information and fails to assemble longer contigs.In this article,we will revisit the major problems of assembling NGS reads on genomic,transcriptomic,metagenomic and metatranscriptomic data.We will also describe our IDBA package for solving these problems.IDBA package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth removal.Compared with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.
基金the National Key R&D Program of China(2022YFC3400300)the National Natural Science Foundation of China(32125009,62172325,32070663)+1 种基金the National Key R&D Program of China(2017YFC0906501)the Key Construction Program of the National‘985’Project,and the Fundamental Research Funds for the Central Universities.
文摘The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and Hi-C.We assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and YH2.0.By comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,respectively.In addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,respectively.Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.
文摘Background:De novo genome assembly relies on two kinds of graphs:de Bruijn graphs and overlap graphs.Overlap graphs are the basis for the Celera assembler,while de Bruijn graphs have become the dominant technical device in the last decade.Those two kinds of graphs are collectively called assembly graphs.Results:In this review,we discuss the most recent advances in the problem of constructing,representing and navigating assembly graphs,focusing on very large datasets.We will also explore some computational techniques,such as the Bloom filter,to compactly store graphs while keeping all functionalities intact.Conclusions:We complete our analysis with a discussion on the algorithmic issues of assembling from long reads(eg.,PacBio and Oxford Nanopore).Finally,we present some of the most relevant open problems in this field.
