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conLSH: Context based Locality Sensitive Hashing for Mapping of noisy SMRT Reads [article]

Angana Chakraborty, Sanghamitra Bandyopadhyay
2019 arXiv   pre-print
It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it.  ...  To deal with the high error probability of SMRT data, a novel contextual Locality Sensitive Hashing (conLSH) based algorithm is proposed in this article, which can effectively align the noisy SMRT reads  ...  ) genomes to extensively study the performance of proposed conLSH-aligner for noisy and long SMRT reads.  ... 
arXiv:1903.04925v1 fatcat:xmjmewzjkzhdpascannid2cqrm

conLSH: Context based Locality Sensitive Hashing for Mapping of noisy SMRT Reads [article]

Angana Chakraborty, Sanghamitra Bandyopadhyay
2019 bioRxiv   pre-print
It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it.  ...  To deal with the high error probability of SMRT data, a novel contextual Locality Sensitive Hashing (conLSH) based algorithm is proposed in this article, which can effectively align the noisy SMRT reads  ...  conLSH-aligner for noisy and long SMRT reads.  ... 
doi:10.1101/574467 fatcat:udc2y3snenawfou4shpc54dn3y

kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on the K-Mer Neighborhood Graph

Ze-Gang Wei, Xing-Guo Fan, Hao Zhang, Xiao-Dan Zhang, Fei Liu, Yu Qian, Shao-Wu Zhang
2022 Frontiers in Genetics  
We introduce kngMap, a novel k-mer neighborhood graph-based mapper that is specifically designed to align long noisy SMS reads to a reference sequence.  ...  However, these long reads contain higher sequencing errors and could more frequently span the breakpoints of structural variants (SVs) than those of shorter reads, leading to many unaligned reads or reads  ...  In this study, we present kngMap, a new, fast, and highly sensitive mapping algorithm for long noisy reads.  ... 
doi:10.3389/fgene.2022.890651 pmid:35601495 pmcid:PMC9117619 fatcat:fqx7lalpencubcqtcku7wnxhme

S-conLSH: alignment-free gapped mapping of noisy long reads

Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay
2021 BMC Bioinformatics  
With multiple spaced patterns, S-conLSH facilitates a gapped mapping of noisy long reads to the corresponding target locations of a reference genome.  ...  The variable-length spaced-seeds or patterns add flexibility to the proposed algorithm by introducing gapped mapping of the noisy long reads.  ...  Specialized methods like BWA-MEM [4] , BLASR [5] , rHAT [6] , Minimap2 [7] , lordFAST [8] , etc., have been designed to align noisy long reads back to the respective reference genomes.  ... 
doi:10.1186/s12859-020-03918-3 pmid:33573603 fatcat:cigva5c3gvazlkjzkgw7tu5u74

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

Ehsan Haghshenas, S Cenk Sahinalp, Faraz Hach, Bonnie Berger
2018 Bioinformatics  
repeat regions.  ...  Unfortunately, because of their high sequencing error rate, reads generated by these technologies are very difficult to work with and cannot be used in many of the standard downstream analysis pipelines  ...  In this paper, we present lordFAST, a fast and highly sensitive mapping tool for long noisy reads. Its sparse anchor extraction strategy has an important impact on the speed of its chaining step.  ... 
doi:10.1093/bioinformatics/bty544 pmid:30561550 pmcid:PMC6298053 fatcat:taphfo4xurcmxb64pavqmeqdgi

S-conLSH: Alignment-free gapped mapping of noisy long reads [article]

Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay
2019 bioRxiv   pre-print
With multiple spaced patterns, S-conLSH facilitates a gapped mapping of noisy long reads to the corresponding target locations of a reference genome.  ...  Therefore, we developed a novel alignment-free method of sequence mapping that is fast and accurate.  ...  Read Mapping: For each noisy long read, S-conLSH utilizes the same hash function for computing the hash values and retrieves sequences of the reference genome that are hashed in the same position as the  ... 
doi:10.1101/801118 fatcat:zmljw6kr5nbkjjxej6v4zn27pi

Technology dictates algorithms: Recent developments in read alignment [article]

Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums (+4 others)
2020 arXiv   pre-print
Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads.  ...  We provide rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read aligners.  ...  . & Wang, Y. rHAT: fast alignment of noisy long reads with regional hashing. Bioinformatics 32, 1625-1631 (2016). 141. Lin, H.-N. & Hsu, W.-L.  ... 
arXiv:2003.00110v3 fatcat:3l3ad4z5xfhjxoo7snaskartxi

Minimap2: pairwise alignment for nucleotide sequences

Heng Li, Inanc Birol
2018 Bioinformatics  
It works with accurate short reads of >100bp in length, >1kb genomic reads at error rate ∼15 full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds  ...  of alignment.  ...  Sedlazeck for pointing out the limitation of BWA-MEM. We are also grateful to minimap2 users who have greatly helped to suggest features and to fix various issues.  ... 
doi:10.1093/bioinformatics/bty191 pmid:29750242 fatcat:c3lhwod4mvglnc4kqrkvsv6kxe

A parallel workflow for online correlation and clique-finding : with applications to finance

Camilo Rostoker
2007
performance with minimal communication overhead.  ...  Finally, we embed our new algorithm within a data processing pipeline that performs high throughput correlation and clique-based clustering of thousands of variables from a high-frequency data stream.  ...  evenly aligned in time.  ... 
doi:10.14288/1.0051985 fatcat:y6det5taebbujf3easucrk7qpa

Towns In Mind: Urban Plans, Political Culture, And Empire In The Colonial Chesapeake, 1607--1722

Paul Musselwhite
2011
Scholars have long asserted that Chesapeake planters' desire for lucre led them to patent huge tracts of land, disperse across the landscape, and completely dismiss urban development.  ...  They shared a desire to urbanize the region, but quarrelled because they had contradictory definitions of precisely what a town was, how it should function, and how it should be governed.  ...  In fact, his work repre<>ented the culmination of a century-long debate about the necessity and practicality of urbanizing the region.  ... 
doi:10.21220/s2-nea8-fd65 fatcat:kbvt2jnrundgbbh3vgl4o4r3pq