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Fast and accurate long-read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin
2010 Computer applications in the biosciences : CABIOS  
Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome  ...  Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error  ...  ACKNOWLEDGEMENTS We are grateful to Zemin Ning for his helpful comments on the SSAHA2 algorithm, and to Kimmo Palin for providing the literature on DAWG.  ... 
doi:10.1093/bioinformatics/btp698 pmid:20080505 pmcid:PMC2828108 fatcat:tawfm7dvebbdhbc2otlpdtfyx4

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

Gabriel A. Al-Ghalith, Emmanuel Montassier, Henry N. Ward, Dan Knights, Jonathan A. Eisen
2016 PLoS Computational Biology  
We present an alternative technique that takes advantage of a high-speed Burrows-Wheeler alignment procedure combined with rapid filtering and parsing of the data to remove bottlenecks in the pipeline.  ...  NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input.  ...  Burrows-Wheeler transform The BWT has received a lot of attention in the alignment of short reads to a reference genome, and now enjoys routine use in clinical and other settings as a well-vetted technique  ... 
doi:10.1371/journal.pcbi.1004658 pmid:26820746 pmcid:PMC4731464 fatcat:vypfem2cefgnrg4baetkrf223y

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads

Elena Y. Harris, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
2012 Computer applications in the biosciences : CABIOS  
We introduce BRAT-BW, a fast, accurate and memoryefficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform).  ...  BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level  ...  ACKNOWLEDGEMENTS We thank F.Krueger for helpful comments and discussions. Funding: NIH R01 AI85077-01A1 and NSF DBI-1062301 (in part). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts264 pmid:22563065 pmcid:PMC3381974 fatcat:7gqu3ic4tnfw5kxnseuhughdcm

Metagenomic Classification using Centrifuge

2019 International journal of recent technology and engineering  
Given a food sample Centrifuge effectively classifies the species present in it enabling a timely and accurate analysis.  ...  Several researches involve various classification techniques and their studies.  ...  Its indexing scheme is based on Burrows-Wheeler transform (BWT) and Ferragina-Manzini index (FM-Index).  ... 
doi:10.35940/ijrte.b3725.078219 fatcat:fik2dshatra2pph22ocxn3slla

Fast and accurate short read alignment with Burrows-Wheeler transform

H. Li, R. Durbin
2009 Bioinformatics  
Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads  ...  Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs.  ...  ACKNOWLEDGEMENTS We are grateful to Mark DePristo and Jared Maguire from the Broad Institute for their suggestions on standardizing the criteria for evaluating alignment programs, and to the three anonymous  ... 
doi:10.1093/bioinformatics/btp324 pmid:19451168 pmcid:PMC2705234 fatcat:7ujsvxic2bfrxos337zvbx54f4

Mapping Billions of Short Reads to a Reference Genome

Jui-Hung Hung, Zhiping Weng
2016 Cold Spring Harbor Protocols  
THE BURROWS-WHEELER (BW) TRANSFORM The BW transform is a technique originally developed for compressing large files and has been adapted to compress genome sequences.  ...  Currently, the most widely used algorithms are all based on the Burrows-Wheeler (BW) transform of the reference genome.  ... 
doi:10.1101/pdb.top093153 pmid:27574203 fatcat:ce62fskuy5aqtb2tlkypnhfrnu

Sequencing Technologies and Analyses: Where Have We Been and Where Are We Going?

Vikas Bansal, Christina Boucher
2019 iScience  
, including linked reads and single-molecule long-read sequencing.  ...  There was an exploration of several traditional topics in sequence analysis, including genome assembly, sequence alignment, and data compression, and development of methods for new sequencing technologies  ...  ACKNOWLEDGMENTS C.B. was funded by the NIH through NIAID grant R01AI141810-01 and by the NSF through grant IIS-1618814.  ... 
doi:10.1016/j.isci.2019.06.035 pmid:31472161 pmcid:PMC6733309 fatcat:cdhue4zggnep5iejcvqfy6ekym

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

Fritz J. Sedlazeck, Philipp Rescheneder, Arndt von Haeseler
2013 Bioinformatics  
Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma.  ...  At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads.  ...  ACKNOWLEDGEMENTS The authors thank Miguel Gallach for help with the manuscript and Hermann Romanek for help with the implementation and helpful discussions.  ... 
doi:10.1093/bioinformatics/btt468 pmid:23975764 fatcat:kdll25pnfzajzkmaghotzskcna

Sense from sequence reads: methods for alignment and assembly

Paul Flicek, Ewan Birney
2009 Nature Methods  
Zerbino and support by the Wellcome Trust and the European Molecular Biology Laboratory.  ...  Over the past year, a new generation of short-read alignment programs including BOWTIE 14 , BWA 15 and SOAP2 (ref. 16 ) have been developed that are based on the Burrows-Wheeler transform (BWT) 17  ...  This Figure 1 | 1 Schematic of a hash table-based alignment strategy. Figure 2 | 2 The Burrows-Wheeler transform for genomic sequence data. © 2009 Nature America, Inc.  ... 
doi:10.1038/nmeth.1376 pmid:19844229 fatcat:mzoo4zw35zg6tku5milvel6cqm

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

Sophie Schbath, Véronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, Jean-François Gibrat
2012 Journal of Computational Biology  
Special attention was paid to reads uniquely reported and to reads with multiple hits.  ...  We built a set of reads that exist in single or multiple copies in a reference genome and for which there is no mismatch, and a set of reads with three mismatches.  ...  Notice that suffix arrays, together with their Burrows-Wheeler transforms, are very compact.  ... 
doi:10.1089/cmb.2012.0022 pmid:22506536 pmcid:PMC3375638 fatcat:wwukslo2bjhyvfp4mqgcibyewi

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim, Ben Langmead, Steven L Salzberg
2015 Nature Methods  
HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment  ...  As RNA-seq has matured, sequencing throughput and read lengths have increased dramatically to 100-500 million reads per run with lengths of 100 bp or longer.  ...  Pertea and L. Song for their invaluable contributions to our discussions on HISAT. We also thank C. Trapnell for the use of his TuxSim simulation program.  ... 
doi:10.1038/nmeth.3317 pmid:25751142 pmcid:PMC4655817 fatcat:rc7o4j2ijnbf7ownpxtv3ryvuy

OSA: a fast and accurate alignment tool for RNA-Seq

Jun Hu, Huanying Ge, Matt Newman, Kejun Liu
2012 Computer applications in the biosciences : CABIOS  
We develop Omicsoft sequence aligner (OSA), a fast and accurate alignment tool for RNA-Seq data.  ...  Accurately mapping RNA-Seq reads to the reference genome is a critical step for performing downstream analysis such as transcript assembly, isoform detection and quantification.  ...  ., 2011) first maps reads to reference genome indexed with Burrows Wheeler transformation (BWT), and then unmapped reads are aligned again using two segment strategies.  ... 
doi:10.1093/bioinformatics/bts294 pmid:22592379 fatcat:33dz3orcija2bdzz6wxojetyhy

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

G. Lunter, M. Goodson
2010 Genome Research  
Acknowledgments We thank David Adams for use of the M. spretus data, Ioannis Ragoussis for use of the MCF7 mRNA-seq data, and Cornelis A. Albers and Zam Iqbal for helpful discussions.  ...  A second category is based on the Burrows-Wheeler transform and associated data structures, which support fast retrieval of long inexact string matches.  ...  Mappers that use the Burrows-Wheeler transform (BWA [Li and Durbin 2009] , SOAP2 ], Bowtie [Langmead et al. 2009 ]) are very fast but tend to be less sensitive than are the best hash-based mappers.  ... 
doi:10.1101/gr.111120.110 pmid:20980556 pmcid:PMC3106326 fatcat:fx7nyywv5vbexi66p7rdu3fc7a

YOABS: yet other aligner of biological sequences—an efficient linearly scaling nucleotide aligner

V. L. Galinsky
2012 Bioinformatics  
However, the choice of long-read aligners effective in terms of both performance and memory are limited and includes only handful of hash table (BLAT, SSAHA2) or trie (Burrows-Wheeler Transform -Smith-Waterman  ...  platforms with long-read mapping.  ...  ACKNOWLEDGEMENT The author is thankful for stimulating discussions with Valentin Shevchenko. The author is also grateful to the reviewers for a number of important comments and suggestions.  ... 
doi:10.1093/bioinformatics/bts102 pmid:22402614 fatcat:7v2jnjm3kvf37ano2l67jzxole

Long Read Alignment with Parallel MapReduce Cloud Platform

Ahmed Abdulhakim Al-Absi, Dae-Ki Kang
2015 BioMed Research International  
Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment.  ...  The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment.  ...  For long read alignment, researchers have proposed Burrows-Wheeler Aligner's Smith-Waterman (BWA-SW) Alignment [10] , Bowtie2 [5] , Cushaw2 [11] , and BWA-MEM [12] .  ... 
doi:10.1155/2015/807407 pmid:26839887 pmcid:PMC4709609 fatcat:ezku2olljbbcdfex2n3dlijpue
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