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Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
2016
Bioinformatics
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Results: We present a new mapper, minimap, and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. ...
Availability and implementation: https://github.com/lh3/minimap and https://github.com/lh3/miniasm Contact: hengli@broadinstitute.org ...
, talks, comments on social media and unpublished works which have greatly influenced and helped the development of minimap and miniasm. ...
doi:10.1093/bioinformatics/btw152
pmid:27153593
pmcid:PMC4937194
fatcat:lde73lu5ozaq7k2544l4x3npoa
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads
[article]
2017
arXiv
pre-print
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2016 pre-print arXiv:1609.07293v1 fatcat:qulo6f547za25ed5lfgkvafscyOther Versions
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. ...
However their high error rate significantly complicates assembly and requires expensive correction steps to layout the reads using standard assembly engines. ...
ACKNOWLEDGEMENT TB would like to thank Genoscope's sequencing (Laboratoire de Séquençage) and bioinformatics (Laboratoire d'Informatique Scientifique) teams for sharing some Acinetobacter baylyi ADP1 and ...
arXiv:1609.07293v3
fatcat:b3yr6tt6vze4ljttje5yx7hkua
Yet another de novo genome assembler
[article]
2019
bioRxiv
pre-print
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We present a new tool, called Ra, for de novo genome assembly of long uncorrected reads. ...
It is a fast and memory friendly assembler based on sequence classification and assembly graphs, developed with large genomes in mind. It is freely available at https://github.com/lbcbsci/ra. ...
Further- [8] Flye ABruijn graph [9] Hinge Repeat-aware BOG [10] Miniasm Assembly graph [6] Wtdbg2 Fuzzy Bruijn graph [11] Algorithm 1 Ra algorithm for de novo genome assembly Input: Set of long ...
doi:10.1101/656306
fatcat:2ebd4czgw5hfjfnjraspbaovgi
Oxford Nanopore MinION genome sequencer: performance characteristics, optimised analysis workflow, phylogenetic analysis and prediction of antimicrobial resistance in Neisseria gonorrhoeae
[article]
2018
bioRxiv
pre-print
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We also show that the ONT-derived sequences can be useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous ...
assemblies and finished reference genomes. ...
Minimap and miniasm: fast mapping and de novo assembly for noisy long 564 sequences. ...
doi:10.1101/349316
fatcat:urudz7w62zgjhbs6htbbhf7igq
Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
[article]
2021
arXiv
pre-print
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Fourth, we propose SeGraM, the first hardware acceleration framework for sequence-to-graph mapping and alignment. ...
First, we comprehensively analyze the tools in the genome assembly pipeline for long reads in multiple dimensions, uncovering bottlenecks and tradeoffs that different combinations of tools and different ...
bp reads) causes errors and ambiguities for read mapping [90, 296] , and poses computational challenges and accuracy problems to de novo assembly [15] . ...
arXiv:2111.01916v1
fatcat:lbwk74jcbjgqzeqk7gnb77asja
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
[article]
2016
bioRxiv
pre-print
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Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. ...
We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. ...
Acknowledgements We thank Celera and Pacific Biosciences for open source software that was critical for the development of Canu, and also John Urban and all other Canu users who provided early testing ...
doi:10.1101/071282
fatcat:hpw4w3oej5hhxaoajd3vxbatle
Oxford Nanopore MinION Sequencing and Genome Assembly
2016
Genomics, Proteomics & Bioinformatics
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for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. ...
While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. ...
Acknowledgments We would like to thank the MinION Analysis and Reference Consortium (MARC) for sharing the ONT data. ...
doi:10.1016/j.gpb.2016.05.004
pmid:27646134
pmcid:PMC5093776
fatcat:6fim4654yncq3pb67nnqquaj6m
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
2017
Genome Research
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Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. ...
We address these issues with Canu, a complete reworking of Celera Assembler that is specifically designed for noisy single-molecule sequences. ...
Acknowledgements We thank Celera and Pacific Biosciences for open source software that was critical for the development of Canu, and also John Urban and all other Canu users who provided early testing ...
doi:10.1101/gr.215087.116
pmid:28298431
pmcid:PMC5411767
fatcat:fvd4olceubbztogj24z2g6zlve
Gapless assembly of maize chromosomes using long read technologies
[article]
2020
bioRxiv
pre-print
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We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs. ...
The B73-Ab10 genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), multiple highly repetitive centromeres and heterochromatic knobs, and 53 Mb of the Ab10 meiotic drive ...
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103-2110 (2016). 15. Du, H. & Liang, C. ...
doi:10.1101/2020.01.14.906230
fatcat:shdmrtwzrzehjd3bdgz4o5x7bi
Alignment-free sequence comparison: benefits, applications, and tools
2017
Genome Biology
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The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. ...
However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. ...
arms) from
third-generation long and noisy reads
(10 kbp) using a dimensionality reduction
technique MinHash
Software (Java) [76]
https://github.com/marbl/
MHAP
Miniasm
Assembler of long noisy ...
doi:10.1186/s13059-017-1319-7
pmid:28974235
pmcid:PMC5627421
fatcat:5s7yd22l7bbmpljqc7fj4cbifm
SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from functional annotations of SNPs, MNPs and InDels
[article]
2021
medRxiv
pre-print
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In a context of SARS-CoV-2 surveillance needed proper and fast assessment of epidemiological clusters from large amount of samples, the present manuscript proposes a workflow for identifying accurately ...
BACKGROUND: Faced to the ongoing global pandemic of coronavirus disease, the 'National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis' (GENPAT) ...
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinforma Oxf Engl. 2016;32:2103-10. 38. Li H. Minimap2: pairwise alignment for nucleotide sequences. ...
doi:10.1101/2021.05.25.21257370
fatcat:nbk2m76c6zgzzmwnid2glahc7m
Modern technologies and algorithms for scaffolding assembled genomes
2019
PLoS Computational Biology
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The computational reconstruction of genome sequences from shotgun sequencing data has been greatly simplified by the advent of sequencing technologies that generate long reads. ...
., bacterial or viral), complete genome sequences can frequently be reconstructed computationally without the need for further experiments. ...
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016; 32(14):2103-10. ...
doi:10.1371/journal.pcbi.1006994
pmid:31166948
pmcid:PMC6550390
fatcat:3cxdpvhs2faifj35iciodxnbt4
A pseudomolecule assembly of the Rocky Mountain elk genome
2021
PLoS ONE
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To overcome this limitation, PacBio, Illumina, and Hi-C sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. ...
Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes ...
for preparation of libraries and DNA sequencing. ...
doi:10.1371/journal.pone.0249899
pmid:33909645
pmcid:PMC8081196
fatcat:dqaa66tzw5cztkyyb5qmrnkoia
MBG: Minimizer-based Sparse de Bruijn Graph Construction
[article]
2020
bioRxiv
pre-print
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Traditionally long read sequencing technologies have had too high error rates for de Bruijn graph-based methods. ...
Recently, HiFi reads have provided a combination of long read length and low error rate, which enables de Bruijn graphs to be used with HiFi reads.ResultsWe have implemented MBG, a tool for building sparse ...
.: Quast: quality assessment tool for genome assemblies. Bioinformatics 29(8), 1072-1075 (2013) [6] Li, H.: Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. ...
doi:10.1101/2020.09.18.303156
fatcat:gipx44vcurestaqmgxifgqybxi
The third generation sequencing: the advanced approach to genetic diseases
2020
Translational Pediatrics
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of the improvement in the bioinformatic analysis for the TGS and its limitations. ...
In recent years, the third generation sequencing (TGS) has been gaining insight into more genetic diseases owing to the single molecular and real time sequencing technology. ...
For example, de novo mutations can occur in the different stage of embryonic development. ...
doi:10.21037/tp.2020.03.06
pmid:32477917
pmcid:PMC7237973
fatcat:m2pn6qg2cvczfaqe7ba67rllku
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