From c2b09356b84355194dbe39272d8227b49df877cf Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 4 Nov 2017 22:19:46 -0400 Subject: [PATCH] moved conclusion to result; need new discussion --- tex/minimap2.bib | 8 ++++++++ tex/minimap2.tex | 17 ++++++++++------- 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/tex/minimap2.bib b/tex/minimap2.bib index bd85dc5..fdc7e35 100644 --- a/tex/minimap2.bib +++ b/tex/minimap2.bib @@ -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}} diff --git a/tex/minimap2.tex b/tex/minimap2.tex index 2017eb8..9ad06ab 100644 --- a/tex/minimap2.tex +++ b/tex/minimap2.tex @@ -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