341 lines
9.7 KiB
BibTeX
341 lines
9.7 KiB
BibTeX
@article{Chaisson:2012aa,
|
|
Author = {Chaisson, Mark J and Tesler, Glenn},
|
|
Journal = {BMC Bioinformatics},
|
|
Pages = {238},
|
|
Title = {{Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory}},
|
|
Volume = {13},
|
|
Year = {2012}}
|
|
|
|
@article{Liu:2016ab,
|
|
Author = {Liu, Bo and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {1625-31},
|
|
Title = {{rHAT}: fast alignment of noisy long reads with regional hashing},
|
|
Volume = {32},
|
|
Year = {2016}}
|
|
|
|
@article{Liu:2017aa,
|
|
Author = {Liu, Bo and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {192-201},
|
|
Title = {{LAMSA}: fast split read alignment with long approximate matches},
|
|
Volume = {33},
|
|
Year = {2017}}
|
|
|
|
@article{Lin:2017aa,
|
|
Author = {Lin, Hsin-Nan and Hsu, Wen-Lian},
|
|
Journal = {Bioinformatics},
|
|
Title = {Kart: a divide-and-conquer algorithm for {NGS} read alignment},
|
|
Year = {2017}}
|
|
|
|
@article{Li:2013aa,
|
|
Author = {Li, Heng},
|
|
Journal = {arXiv:1303.3997},
|
|
Title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
|
|
archivePrefix = "arXiv",
|
|
eprint = {1303.3997},
|
|
primaryClass = "q-bio",
|
|
Year = {2013}}
|
|
|
|
@article{Sovic:2016aa,
|
|
Author = {Sovi{\'c}, Ivan and others},
|
|
Journal = {Nat Commun},
|
|
Pages = {11307},
|
|
Title = {Fast and sensitive mapping of nanopore sequencing reads with {GraphMap}},
|
|
Volume = {7},
|
|
Year = {2016}}
|
|
|
|
@article{Langmead:2012fk,
|
|
Author = {Langmead, Ben and Salzberg, Steven L},
|
|
Journal = {Nat Methods},
|
|
Pages = {357-9},
|
|
Title = {Fast gapped-read alignment with {Bowtie} 2},
|
|
Volume = {9},
|
|
Year = {2012}}
|
|
|
|
@article{Li:2016aa,
|
|
Author = {Li, Heng},
|
|
Journal = {Bioinformatics},
|
|
Pages = {2103-10},
|
|
Title = {Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences},
|
|
Volume = {32},
|
|
Year = {2016}}
|
|
|
|
@misc{Ruan:2016,
|
|
title = {Ultra-fast de novo assembler using long noisy reads},
|
|
author = {Jue Ruan},
|
|
journal = {Unpulished},
|
|
howpublished = {\href{https://github.com/ruanjue/smartdenovo}{https://github.com/ruanjue/smartdenovo}},
|
|
year = {2016}}
|
|
|
|
@article{Miller:1988aa,
|
|
Author = {Miller, W and Myers, E W},
|
|
Journal = {Bull Math Biol},
|
|
Number = {2},
|
|
Pages = {97-120},
|
|
Title = {Sequence comparison with concave weighting functions},
|
|
Volume = {50},
|
|
Year = {1988}}
|
|
|
|
@article{Gotoh:1990aa,
|
|
Author = {Gotoh, O},
|
|
Journal = {Bull Math Biol},
|
|
Pages = {359-73},
|
|
Title = {Optimal sequence alignment allowing for long gaps},
|
|
Volume = {52},
|
|
Year = {1990}}
|
|
|
|
@article{Wu:1996aa,
|
|
Author = {Wu, Sun and others},
|
|
Journal = {Algorithmica},
|
|
Pages = {50-67},
|
|
Title = {A subquadratic algorithm for approximate limited expression matching},
|
|
Volume = {15},
|
|
Year = {1996}}
|
|
|
|
@article{Daily:2016aa,
|
|
Author = {Daily, Jeff},
|
|
Journal = {BMC Bioinformatics},
|
|
Month = {Feb},
|
|
Pages = {81},
|
|
Title = {Parasail: {SIMD C} library for global, semi-global, and local pairwise sequence alignments},
|
|
Volume = {17},
|
|
Year = {2016}}
|
|
|
|
@article{Sedlazeck169557,
|
|
author = {Sedlazeck, Fritz J and others},
|
|
title = {Accurate detection of complex structural variations using single molecule sequencing},
|
|
note = {doi:10.1101/169557},
|
|
journal = {bioRxiv},
|
|
year = {2017}}
|
|
|
|
@article{Altschul:1997vn,
|
|
Author = {Altschul, S F and others},
|
|
Journal = {Nucleic Acids Res},
|
|
Pages = {3389-402},
|
|
Title = {Gapped {BLAST} and {PSI-BLAST}: a new generation of protein database search programs},
|
|
Volume = {25},
|
|
Year = {1997}}
|
|
|
|
@article{Sosic:2017aa,
|
|
Author = {{\v S}o{\v s}i\'{c}, Martin and {\v S}ikic, Mile},
|
|
Journal = {Bioinformatics},
|
|
Pages = {1394-1395},
|
|
Title = {Edlib: a {C/C++} library for fast, exact sequence alignment using edit distance},
|
|
Volume = {33},
|
|
Year = {2017}}
|
|
|
|
@article{Abouelhoda:2005aa,
|
|
Author = {Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
|
|
Journal = {J. Discrete Algorithms},
|
|
Pages = {321-41},
|
|
Title = {Chaining algorithms for multiple genome comparison},
|
|
Volume = {3},
|
|
Year = {2005}}
|
|
|
|
@article{Ono:2013aa,
|
|
Author = {Ono, Yukiteru and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {119-21},
|
|
Title = {{PBSIM}: {PacBio} reads simulator--toward accurate genome assembly},
|
|
Volume = {29},
|
|
Year = {2013}}
|
|
|
|
@article {Jain128835,
|
|
author = {Jain, Miten and others},
|
|
title = {Nanopore sequencing and assembly of a human genome with ultra-long reads},
|
|
year = {2017},
|
|
note = {doi:10.1101/128835},
|
|
publisher = {Cold Spring Harbor Labs Journals},
|
|
journal = {bioRxiv}}
|
|
|
|
@article{Lau:2016aa,
|
|
Author = {Lau, Bayo and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {3829-3832},
|
|
Title = {{LongISLND}: in silico sequencing of lengthy and noisy datatypes},
|
|
Volume = {32},
|
|
Year = {2016}}
|
|
|
|
@article{Robinson:2011aa,
|
|
Author = {Robinson, James T and others},
|
|
Journal = {Nat Biotechnol},
|
|
Pages = {24-6},
|
|
Title = {Integrative genomics viewer},
|
|
Volume = {29},
|
|
Year = {2011}}
|
|
|
|
@article{Gotoh:1982aa,
|
|
Author = {Gotoh, O},
|
|
Journal = {J Mol Biol},
|
|
Pages = {705-8},
|
|
Title = {An improved algorithm for matching biological sequences},
|
|
Volume = {162},
|
|
Year = {1982}}
|
|
|
|
@article{Altschul:1986aa,
|
|
Author = {Altschul, S F and Erickson, B W},
|
|
Journal = {Bull Math Biol},
|
|
Pages = {603-16},
|
|
Title = {Optimal sequence alignment using affine gap costs},
|
|
Volume = {48},
|
|
Year = {1986}}
|
|
|
|
@article{Wu:2005vn,
|
|
Author = {Wu, Thomas D and Watanabe, Colin K},
|
|
Journal = {Bioinformatics},
|
|
Pages = {1859-75},
|
|
Title = {{GMAP}: a genomic mapping and alignment program for {mRNA} and {EST} sequences},
|
|
Volume = {21},
|
|
Year = {2005}}
|
|
|
|
@article{Iwata:2012aa,
|
|
Author = {Iwata, Hiroaki and Gotoh, Osamu},
|
|
Journal = {Nucleic Acids Res},
|
|
Pages = {e161},
|
|
Title = {Benchmarking spliced alignment programs including {Spaln2}, an extended version of {Spaln} that incorporates additional species-specific features},
|
|
Volume = {40},
|
|
Year = {2012}}
|
|
|
|
@article{Dobin:2013kx,
|
|
Author = {Dobin, Alexander and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {15-21},
|
|
Title = {{STAR}: ultrafast universal {RNA-seq} aligner},
|
|
Volume = {29},
|
|
Year = {2013}}
|
|
|
|
@article{Byrne:2017aa,
|
|
Author = {Byrne, Ashley and others},
|
|
Journal = {Nat Commun},
|
|
Pages = {16027},
|
|
Title = {Nanopore long-read {RNAseq} reveals widespread transcriptional variation among the surface receptors of individual {B} cells},
|
|
Volume = {8},
|
|
Year = {2017}}
|
|
|
|
@article{Roberts:2004fv,
|
|
Author = {Roberts, Michael and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {3363-9},
|
|
Title = {Reducing storage requirements for biological sequence comparison},
|
|
Volume = {20},
|
|
Year = {2004}}
|
|
|
|
@article{Zhang:2006aa,
|
|
Author = {Zhang, Miao and Gish, Warren},
|
|
Journal = {Bioinformatics},
|
|
Pages = {13-20},
|
|
Title = {Improved spliced alignment from an information theoretic approach},
|
|
Volume = {22},
|
|
Year = {2006}}
|
|
|
|
@article{Li:2007aa,
|
|
Author = {Li, Heng and others},
|
|
Journal = {BMC Bioinformatics},
|
|
Pages = {349},
|
|
Title = {A cross-species alignment tool {(CAT)}},
|
|
Volume = {8},
|
|
Year = {2007}}
|
|
|
|
@article{Farrar:2007hs,
|
|
Author = {Farrar, Michael},
|
|
Journal = {Bioinformatics},
|
|
Pages = {156-61},
|
|
Title = {{Striped Smith-Waterman speeds database searches six times over other SIMD implementations}},
|
|
Volume = {23},
|
|
Year = {2007}}
|
|
|
|
@techreport{Holtgrewe:2010aa,
|
|
Address = {Freie Universit{\"a}t Berlin},
|
|
Author = {Holtgrewe, M.},
|
|
Institution = {Institut f{\"u}r Mathematik und Informatik},
|
|
Number = {TR-B-10-06},
|
|
Title = {Mason -- a read simulator for second generation sequencing data},
|
|
Year = {2010}}
|
|
|
|
@article{Zaharia:2011aa,
|
|
Author = {Zaharia, Matei and others},
|
|
Journal = {arXiv:1111:5572},
|
|
Title = {Faster and More Accurate Sequence Alignment with {SNAP}},
|
|
Year = {2011}}
|
|
|
|
@article{Irimia:2008aa,
|
|
Author = {Irimia, Manuel and Roy, Scott William},
|
|
Journal = {PLoS Genet},
|
|
Pages = {e1000148},
|
|
Title = {Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome},
|
|
Volume = {4},
|
|
Year = {2008}}
|
|
|
|
@article{Depristo:2011vn,
|
|
Author = {Depristo, Mark A and others},
|
|
Journal = {Nat Genet},
|
|
Pages = {491-8},
|
|
Title = {A framework for variation discovery and genotyping using next-generation {DNA} sequencing data},
|
|
Volume = {43},
|
|
Year = {2011}}
|
|
|
|
@article{Kurtz:2004zr,
|
|
Author = {Kurtz, Stefan and others},
|
|
Journal = {Genome Biol},
|
|
Pages = {R12},
|
|
Title = {Versatile and open software for comparing large genomes},
|
|
Volume = {5},
|
|
Year = {2004}}
|
|
|
|
@article {Li223297,
|
|
author = {Li, Heng and others},
|
|
title = {New synthetic-diploid benchmark for accurate variant calling evaluation},
|
|
year = {2017},
|
|
note = {doi:10.1101/223297},
|
|
journal = {bioRxiv}
|
|
}
|
|
|
|
@article{Berlin:2015xy,
|
|
Author = {Berlin, Konstantin and others},
|
|
Journal = {Nat Biotechnol},
|
|
Pages = {623-30},
|
|
Title = {Assembling large genomes with single-molecule sequencing and locality-sensitive hashing},
|
|
Volume = {33},
|
|
Year = {2015}}
|
|
|
|
@article{Gurevich:2013aa,
|
|
Author = {Gurevich, Alexey and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {1072-5},
|
|
Title = {{QUAST}: quality assessment tool for genome assemblies},
|
|
Volume = {29},
|
|
Year = {2013}}
|
|
|
|
@article{Li:2010fk,
|
|
Author = {Li, Heng and Durbin, Richard},
|
|
Journal = {Bioinformatics},
|
|
Pages = {589-95},
|
|
Title = {Fast and accurate long-read alignment with {Burrows-Wheeler} transform},
|
|
Volume = {26},
|
|
Year = {2010}}
|
|
|
|
@article{Marcais:2018aa,
|
|
Author = {Mar{\c c}ais, Guillaume and others},
|
|
Journal = {PLoS Comput Biol},
|
|
Pages = {e1005944},
|
|
Title = {{MUMmer4}: A fast and versatile genome alignment system},
|
|
Volume = {14},
|
|
Year = {2018}}
|
|
|
|
@article{Li:2009ys,
|
|
Author = {Li, Heng and others},
|
|
Journal = {Bioinformatics},
|
|
Pages = {2078-9},
|
|
Title = {The {Sequence Alignment/Map format and SAMtools}},
|
|
Volume = {25},
|
|
Year = {2009}}
|
|
|
|
@article{Suzuki:2018aa,
|
|
Author = {Suzuki, Hajime and Kasahara, Masahiro},
|
|
Journal = {BMC Bioinformatics},
|
|
Pages = {45},
|
|
Title = {Introducing difference recurrence relations for faster semi-global alignment of long sequences},
|
|
Volume = {19},
|
|
Year = {2018}}
|