moved conclusion to result; need new discussion
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Title = {A framework for variation discovery and genotyping using next-generation {DNA} sequencing data},
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Volume = {43},
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Year = {2011}}
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@article{Kurtz:2004zr,
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Author = {Kurtz, Stefan and others},
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Journal = {Genome Biol},
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Pages = {R12},
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Title = {Versatile and open software for comparing large genomes},
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Volume = {5},
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Year = {2004}}
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@ -555,16 +555,19 @@ similar INDEL FPPM (both 1.0). In comparison, Bowtie2 has a SNP FNR of 4.7\%
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and INDEL FNR of 10.4\%. Minimap2 is broadly similar to BWA-MEM in the context
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of small variant calling.
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\subsection{Other applications}
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Minimap2 retains minimap's functionality to find overlaps between long reads
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and to search against huge multi-species databases such as \emph{nt} from NCBI.
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Minimap2 can also align similar genomes or different assemblies of the same
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species. It took 7 wall-clock minutes over 8 CPU cores to align a human SMRT
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assembly (AC:GCA\_001297185.1) to GRCh38, over 20 times as fast as
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MUMmer4~\citep{Kurtz:2004zr}.
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\section{Conclusion}
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Minimap2 is a fast, accurate and versatile aligner for long nucleotide
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sequences. In addition to reference-based read mapping, minimap2 inherits
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minimap's functionality to search against huge multi-species databases and to
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find read overlaps. On a few test data sets, minimap2 appears to yield slightly
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better miniasm assembly~\citep{Li:2016aa}. Minimap2 can also align similar
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genomes or different assemblies of the same species. However, full-genome
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alignment is an intricate research topic. More thorough evaluations would be
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necessary to justify the use of minimap2 for such applications.
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sequences.
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\section*{Acknowledgements}
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We owe a debt of gratitude to H. Suzuki and M. Kasahara for releasing their
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