三代比对软件-ngmlr
软件名：ngmlr
版本号：ngmlr 0.2.6
NextGenMap-LR(ngmlr)主要用于三代测序的长reads（PacBio 、Oxford Nanopore）与参考基因组的比对。三代测序产生的reads主要特征有两个：1，读长很长（平均10K）；2，高错误率（10% to 15% for PacBio, and 5% to 20% for Oxford Nanopore sequencing)。NGMLR( https://github.com/philres/ngmlr )是一款为长reads设计的快速且高精度的进行比对的软件，它是基于NGM（seed-and-extend short read aligner）开发的，该软件扩展了segmented convex gap-cost scoring model来适应高错误率的长reads比对。
网址： https://github.com/philres/ngmlr
-r 参考基因组
-q待比对三代测序数据
-o 输出文件
Usage: ngmlr [options] -r
<reference> -q <reads> [-o <output>]
Input/Output:
General:
Advanced:
结果以Sam格式展示：
1， 该软件会在参考基因组所在目录下建一个索引，所以参考基因组所在目录需要有可写权限（也可使用 --skip-write 参数，明确不将 index 写入磁盘 ）；
2， 为参考基因组建立index会耗用很长时间，建议在database（参考基因组所在文件夹）中建立一套index，每次调用。
Accurate detection of complex structural variations using single molecule sequencing
FritzJ Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, ArndtvonHaeseler, Michael Schatz. bioRxiv 169557; doi: https://doi.org/10.1101/169557
Poster & Talks:
Accurate and fast detection of complex and nested structural variations using long read technologies Biological Data Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 26 - 29.10.2016
NGMLR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK,19.09.-2.09.2016
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