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Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Heng Li
2016 Bioinformatics  
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  , talks, comments on social media and unpublished works which have greatly influenced and helped the development of minimap and miniasm.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]

Antoine Recanati, Thomas Brüls, Alexandre d'Aspremont
2017 arXiv   pre-print
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]

Robert Vaser, Mile Sikic
2019 bioRxiv   pre-print
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]

Daniel Golparian, Valentina Dona, Leonor Sanchez-Buso, Sunniva Foerster, Simon Harris, Andrea Endimiani, Nicola Low, Magnus Unemo
2018 bioRxiv   pre-print
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]

Damla Senol Cali
2021 arXiv   pre-print
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]

Sergey Koren, Brian P. Walenz, Konstantin Berlin, Jason R. Miller, Nicholas H. Bergman, Adam M. Phillippy
2016 bioRxiv   pre-print
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

Hengyun Lu, Francesca Giordano, Zemin Ning
2016 Genomics, Proteomics & Bioinformatics  
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

Sergey Koren, Brian P. Walenz, Konstantin Berlin, Jason R. Miller, Nicholas H. Bergman, Adam M. Phillippy
2017 Genome Research  
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]

Kelly Dawe, Jianing Liu, Arun S Seetharam, Kapeel Chougule, Shujun Ou, Kyle William Swentowsky, Jonathan Isaiah Gent, Victor Llaca, Margaret Woodhouse, Nancy Manchanda, Gernot G Presting, David Kudrna (+6 others)
2020 bioRxiv   pre-print
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

Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M. Karlowski
2017 Genome Biology  
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]

Adriano Di Pasquale, Nicolas Radomski, Iolanda Mangone, Paolo Calistri, Alessio Lorusso, Cesare Camma
2021 medRxiv   pre-print
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

Jay Ghurye, Mihai Pop, Nicola Segata
2019 PLoS Computational Biology  
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

Rick E Masonbrink, David Alt, Darrell O Bayles, Paola Boggiatto, William Edwards, Fred Tatum, Jeffrey Williams, Jennifer Wilson-Welder, Aleksey Zimin, Andrew Severin, Steven Olsen
2021 PLoS ONE  
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]

Mikko Rautiainen, Tobias Marschall
2020 bioRxiv   pre-print
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

Tiantian Xiao, Wenhao Zhou
2020 Translational Pediatrics  
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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