软件名：ngmlr

版本号：ngmlr 0.2.6

1. 软件用途综述

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

2. 分析原理

image

Identifyinitial anchors
Verifyanchors with vectorized Smith-Waterman algorithm (scores only)
Filteranchors and find candidate regions for the alignments
Compute thefull alignment between the read and the respective candidate reference regions

3. 实现方法

3.1 使用示例

  ngmlr -r ucsc.hg19.fasta -q XXX.fastq -o YYY.bam

3.2 程序说明

-r 参考基因组

-q待比对三代测序数据

-o 输出文件

3.3软件参数说明

Usage: ngmlr [options] -r

<reference> -q <reads> [-o <output>]

Input/Output:

-r , --reference *（所在路径需要可写权限）

   (required)  Path to the reference genome (FASTA/Q, can begzipped)*

-q , --query*

   Path to the read file(FASTA/Q) [/dev/stdin]*

-o , --output*
```
   Path to output file[stdout]*
```
--skip-write*

   Don't write referenceindex to disk [false]*

--bam-fix*

   Report reads with > 64kCIGAR operations as unmapped. Required to be compatibel to BAM format [false]*

General:

-t , --threads*
```
   Number of threads [1]*
```
-x , --presets*

   Parameter presets fordifferent sequencing technologies [pacbio]*

-i <0-1>, --min-identity <0-1>*

   Alignments with anidentity lower than this threshold will be discarded [0.65]*

-R , --min-residues*

   Alignments containingless than or ( * read length) residues will bediscarded [0.25]*

--no-smallinv*

   Don't detect smallinversions [false]*

--no-lowqualitysplit*

   Split alignments withpoor quality [false]*

--verbose*
```
   Debug output [false]*
```
--no-progress*

   Don't print progress infowhile mapping [false]*

Advanced:

--match*
```
   Match score [2]*
```
--mismatch*
```
   Mismatch score [-5]*
```
--gap-open*
```
   Gap open score [-5]*
```
--gap-extend-max*
```
   Gap open extend max [-5]*
```
--gap-extend-min*
```
   Gap open extend min [-1]*
```
--gap-decay*
```
   Gap extend decay [0.15]*
```
-k <10-15>, --kmer-length <10-15>*
```
   K-mer length in bases[13]*
```
--kmer-skip*

   Number of k-mers to skipwhen building the lookup table from the reference [2]*

--bin-size*

   Sets the size of the gridused during candidate search [4]*

--max-segments*

   Max number of segmentsallowed for a read per kb [1]*

--subread-length*

   Length of fragments readsare split into [256]*

--subread-corridor*

   Length of corridorsub-reads are aligned with [40]*

3.4 结果展示及说明

结果以Sam格式展示：

image.png

4.资源消耗

image.png

5.注意事项

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。

6.软件相关文献引用

Accurate detection of complex structural variations using single molecule sequencing

FritzJ Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, ArndtvonHaeseler, Michael Schatz.bioRxiv169557; doi: https://doi.org/10.1101/169557

7. FAQs

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 generationsequencing reads for improved structural variation analysis Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK,19.09.-2.09.2016

三代比对软件-ngmlr