104 lines
3.0 KiB
BibTeX
104 lines
3.0 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 Guan, Dengfeng and Teng, Mingxiang and Wang, Yadong},
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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 Gao, Yan and Wang, Yadong},
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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 = {0902.0885},
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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 {\v S}iki{\'c}, Mile and Wilm, Andreas and Fenlon, Shannon Nicole and Chen, Swaine 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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@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 Manber, U and Myers, Gene},
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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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