284 lines
8.1 KiB
BibTeX
284 lines
8.1 KiB
BibTeX
@article{Chaisson:2012aa,
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Author = {Chaisson, Mark J and Tesler, Glenn},
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Journal = {BMC Bioinformatics},
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Pages = {238},
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Title = {{Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory}},
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Volume = {13},
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Year = {2012}}
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@article{Liu:2016ab,
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Author = {Liu, Bo and others},
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Journal = {Bioinformatics},
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Pages = {1625-31},
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Title = {{rHAT}: fast alignment of noisy long reads with regional hashing},
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Volume = {32},
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Year = {2016}}
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@article{Liu:2017aa,
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Author = {Liu, Bo and others},
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Journal = {Bioinformatics},
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Pages = {192-201},
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Title = {{LAMSA}: fast split read alignment with long approximate matches},
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Volume = {33},
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Year = {2017}}
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@article{Lin:2017aa,
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Author = {Lin, Hsin-Nan and Hsu, Wen-Lian},
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Journal = {Bioinformatics},
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Title = {Kart: a divide-and-conquer algorithm for {NGS} read alignment},
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Year = {2017}}
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@article{Li:2013aa,
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Author = {Li, Heng},
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Journal = {arXiv:1303.3997},
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Title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
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archivePrefix = "arXiv",
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eprint = {1303.3997},
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primaryClass = "q-bio",
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Year = {2013}}
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@article{Sovic:2016aa,
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Author = {Sovi{\'c}, Ivan and others},
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Journal = {Nat Commun},
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Pages = {11307},
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Title = {Fast and sensitive mapping of nanopore sequencing reads with {GraphMap}},
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Volume = {7},
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Year = {2016}}
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@article{Langmead:2012fk,
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Author = {Langmead, Ben and Salzberg, Steven L},
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Journal = {Nat Methods},
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Pages = {357-9},
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Title = {Fast gapped-read alignment with {Bowtie} 2},
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Volume = {9},
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Year = {2012}}
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@article{Li:2016aa,
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Author = {Li, Heng},
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Journal = {Bioinformatics},
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Pages = {2103-10},
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Title = {Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences},
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Volume = {32},
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Year = {2016}}
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@misc{Suzuki:2016,
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title = {Fast and accurate alignment tool for PacBio and Nanopore long reads},
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author = {Hajime Suzuki},
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journal = {Unpublished},
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howpublished = {\href{https://github.com/ocxtal/minialign}{https://github.com/ocxtal/minialign}},
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year = {2016}}
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@misc{Ruan:2016,
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title = {Ultra-fast de novo assembler using long noisy reads},
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author = {Jue Ruan},
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journal = {Unpulished},
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howpublished = {\href{https://github.com/ruanjue/smartdenovo}{https://github.com/ruanjue/smartdenovo}},
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year = {2016}}
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@article{Miller:1988aa,
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Author = {Miller, W and Myers, E W},
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Journal = {Bull Math Biol},
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Number = {2},
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Pages = {97-120},
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Title = {Sequence comparison with concave weighting functions},
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Volume = {50},
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Year = {1988}}
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@article{Gotoh:1990aa,
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Author = {Gotoh, O},
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Journal = {Bull Math Biol},
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Pages = {359-73},
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Title = {Optimal sequence alignment allowing for long gaps},
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Volume = {52},
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Year = {1990}}
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@article{Wu:1996aa,
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Author = {Wu, Sun and others},
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Journal = {Algorithmica},
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Pages = {50-67},
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Title = {A subquadratic algorithm for approximate limited expression matching},
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Volume = {15},
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Year = {1996}}
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@article{Daily:2016aa,
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Author = {Daily, Jeff},
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Journal = {BMC Bioinformatics},
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Month = {Feb},
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Pages = {81},
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Title = {Parasail: {SIMD C} library for global, semi-global, and local pairwise sequence alignments},
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Volume = {17},
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Year = {2016}}
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@article{Sedlazeck169557,
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author = {Sedlazeck, Fritz J and others},
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title = {Accurate detection of complex structural variations using single molecule sequencing},
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note = {doi:10.1101/169557},
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journal = {bioRxiv},
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year = {2017}}
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@article{Altschul:1997vn,
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Author = {Altschul, S F and others},
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Journal = {Nucleic Acids Res},
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Pages = {3389-402},
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Title = {Gapped {BLAST} and {PSI-BLAST}: a new generation of protein database search programs},
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Volume = {25},
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Year = {1997}}
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@article{Sosic:2017aa,
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Author = {{\v S}o{\v s}i\'{c}, Martin and {\v S}ikic, Mile},
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Journal = {Bioinformatics},
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Pages = {1394-1395},
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Title = {Edlib: a {C/C++} library for fast, exact sequence alignment using edit distance},
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Volume = {33},
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Year = {2017}}
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@article{Abouelhoda:2005aa,
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Author = {Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
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Journal = {J. Discrete Algorithms},
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Pages = {321-41},
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Title = {Chaining algorithms for multiple genome comparison},
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Volume = {3},
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Year = {2005}}
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@article{Ono:2013aa,
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Author = {Ono, Yukiteru and others},
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Journal = {Bioinformatics},
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Pages = {119-21},
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Title = {{PBSIM}: {PacBio} reads simulator--toward accurate genome assembly},
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Volume = {29},
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Year = {2013}}
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@article {Jain128835,
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author = {Jain, Miten and others},
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title = {Nanopore sequencing and assembly of a human genome with ultra-long reads},
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year = {2017},
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note = {doi:10.1101/128835},
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publisher = {Cold Spring Harbor Labs Journals},
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journal = {bioRxiv}}
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@article{Lau:2016aa,
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Author = {Lau, Bayo and others},
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Journal = {Bioinformatics},
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Pages = {3829-3832},
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Title = {{LongISLND}: in silico sequencing of lengthy and noisy datatypes},
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Volume = {32},
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Year = {2016}}
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@article{Robinson:2011aa,
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Author = {Robinson, James T and others},
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Journal = {Nat Biotechnol},
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Pages = {24-6},
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Title = {Integrative genomics viewer},
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Volume = {29},
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Year = {2011}}
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@article {Suzuki130633,
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author = {Suzuki, Hajime and Kasahara, Masahiro},
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title = {Acceleration Of Nucleotide Semi-Global Alignment With Adaptive Banded Dynamic Programming},
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year = {2017},
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note = {doi:10.1101/130633},
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publisher = {Cold Spring Harbor Labs Journals},
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journal = {bioRxiv}}
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@article{Gotoh:1982aa,
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Author = {Gotoh, O},
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Journal = {J Mol Biol},
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Pages = {705-8},
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Title = {An improved algorithm for matching biological sequences},
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Volume = {162},
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Year = {1982}}
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@article{Altschul:1986aa,
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Author = {Altschul, S F and Erickson, B W},
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Journal = {Bull Math Biol},
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Pages = {603-16},
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Title = {Optimal sequence alignment using affine gap costs},
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Volume = {48},
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Year = {1986}}
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@article{Wu:2005vn,
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Author = {Wu, Thomas D and Watanabe, Colin K},
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Journal = {Bioinformatics},
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Pages = {1859-75},
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Title = {{GMAP}: a genomic mapping and alignment program for {mRNA} and {EST} sequences},
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Volume = {21},
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Year = {2005}}
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@article{Iwata:2012aa,
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Author = {Iwata, Hiroaki and Gotoh, Osamu},
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Journal = {Nucleic Acids Res},
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Pages = {e161},
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Title = {Benchmarking spliced alignment programs including {Spaln2}, an extended version of {Spaln} that incorporates additional species-specific features},
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Volume = {40},
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Year = {2012}}
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@article{Dobin:2013kx,
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Author = {Dobin, Alexander and others},
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Journal = {Bioinformatics},
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Pages = {15-21},
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Title = {{STAR}: ultrafast universal {RNA-seq} aligner},
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Volume = {29},
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Year = {2013}}
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@article{Byrne:2017aa,
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Author = {Byrne, Ashley and others},
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Journal = {Nat Commun},
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Pages = {16027},
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Title = {Nanopore long-read {RNAseq} reveals widespread transcriptional variation among the surface receptors of individual {B} cells},
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Volume = {8},
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Year = {2017}}
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@article{Roberts:2004fv,
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Author = {Roberts, Michael and others},
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Journal = {Bioinformatics},
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Pages = {3363-9},
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Title = {Reducing storage requirements for biological sequence comparison},
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Volume = {20},
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Year = {2004}}
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@article{Zhang:2006aa,
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Author = {Zhang, Miao and Gish, Warren},
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Journal = {Bioinformatics},
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Pages = {13-20},
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Title = {Improved spliced alignment from an information theoretic approach},
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Volume = {22},
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Year = {2006}}
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@article{Li:2007aa,
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Author = {Li, Heng and others},
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Journal = {BMC Bioinformatics},
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Pages = {349},
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Title = {A cross-species alignment tool {(CAT)}},
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Volume = {8},
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Year = {2007}}
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@article{Farrar:2007hs,
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Author = {Farrar, Michael},
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Journal = {Bioinformatics},
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Pages = {156-61},
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Title = {{Striped Smith-Waterman speeds database searches six times over other SIMD implementations}},
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Volume = {23},
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Year = {2007}}
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@techreport{Holtgrewe:2010aa,
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Address = {Freie Universit{\"a}t Berlin},
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Author = {Holtgrewe, M.},
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Institution = {Institut f{\"u}r Mathematik und Informatik},
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Number = {TR-B-10-06},
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Title = {Mason -- a read simulator for second generation sequencing data},
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Year = {2010}}
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@article{Langmead:2012fk,
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Author = {Langmead, Ben and Salzberg, Steven L},
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Journal = {Nat Methods},
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Pages = {357-9},
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Title = {Fast gapped-read alignment with Bowtie 2},
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Volume = {9},
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Year = {2012}}
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@article{Zaharia:2011aa,
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Author = {Zaharia, Matei and others},
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Journal = {arXiv:1111:5572},
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Title = {Faster and More Accurate Sequence Alignment with SNAP},
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Year = {2011}}
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