moved conclusion to result; need new discussion

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Heng Li 2017-11-04 22:19:46 -04:00
parent a3f0aa1d5b
commit c2b09356b8
2 changed files with 18 additions and 7 deletions

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@ -297,3 +297,11 @@
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}}

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