Accurate high throughput alignment via line sweep-based seed processing

[1]  Chirag Jain,et al.  A fast adaptive algorithm for computing whole-genome homology maps , 2018, bioRxiv.

[2]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[3]  Michael C. Schatz,et al.  Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.

[4]  Masahiro Kasahara,et al.  Acceleration of Nucleotide Semi-Global Alignment with Adaptive Banded Dynamic Programming , 2017, bioRxiv.

[5]  R. Myers,et al.  Advancements in Next-Generation Sequencing. , 2016, Annual review of genomics and human genetics.

[6]  Yongchao Liu,et al.  Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data , 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[7]  Niranjan Nagarajan,et al.  Fast and sensitive mapping of nanopore sequencing reads with GraphMap , 2016, Nature Communications.

[8]  Carl Kingsford,et al.  Fast Search of Thousands of Short-Read Sequencing Experiments , 2015, Nature Biotechnology.

[9]  Alexa B. R. McIntyre,et al.  Extensive sequencing of seven human genomes to characterize benchmark reference materials , 2015, Scientific Data.

[10]  Ying Chen,et al.  High speed BLASTN: an accelerated MegaBLAST search tool , 2015, Nucleic acids research.

[11]  William R Pearson,et al.  An Introduction to Sequence Similarity (“Homology”) Searching , 2013, Current protocols in bioinformatics.

[12]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[13]  Roderic Guigó,et al.  The GEM mapper: fast, accurate and versatile alignment by filtration , 2012, Nature Methods.

[14]  Glenn Tesler,et al.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory , 2012, BMC Bioinformatics.

[15]  Heng Li,et al.  Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly , 2012, Bioinform..

[16]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[17]  Satinderjit Singh,et al.  An Alternate Algorithm for (3x3) Median Filtering of Digital Images , 2012, BIOINFORMATICS 2012.

[18]  Heng Li,et al.  A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..

[19]  Jared T. Simpson,et al.  Efficient construction of an assembly string graph using the FM-index , 2010, Bioinform..

[20]  Paul Flicek,et al.  Sense from sequence reads: methods for alignment and assembly , 2009, Nature Methods.

[21]  Siu-Ming Yiu,et al.  High Throughput Short Read Alignment via Bi-directional BWT , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine.

[22]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[23]  Wing Hung Wong,et al.  SeqMap: mapping massive amount of oligonucleotides to the genome , 2008, Bioinform..

[24]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[25]  Enno Ohlebusch,et al.  Chaining algorithms for multiple genome comparison , 2005, J. Discrete Algorithms.

[26]  Michael Roberts,et al.  Reducing storage requirements for biological sequence comparison , 2004, Bioinform..

[27]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[28]  Enno Ohlebusch,et al.  Replacing suffix trees with enhanced suffix arrays , 2004, J. Discrete Algorithms.

[29]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[30]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

[31]  Tetsuo Shibuya,et al.  Match Chaining Algorithms for cDNA Mapping , 2003, WABI.

[32]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[33]  Eugene W. Myers,et al.  Chaining multiple-alignment fragments in sub-quadratic time , 1995, SODA '95.

[34]  O. Gotoh.  An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[35]  Robert C. Bolles,et al.  Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography , 1981, CACM.

[36]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[37]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[38]  W R Pearson,et al.  Flexible sequence similarity searching with the FASTA3 program package. , 2000, Methods in molecular biology.

[39]  Balaji Raghavachari,et al.  Chaining Multiple-Alignment Blocks , 1994, J. Comput. Biol..

[40]  O. Gotoh,et al.  Optimal sequence alignment allowing for long gaps. , 1990, Bulletin of mathematical biology.

[41]  Ronald L. Rivest,et al.  Introduction to Algorithms , 1990 .

[42]  O. Gotoh,et al.  Optimal sequence alignment allowing for long gaps , 1990 .