MapNext:推荐一款可以用于做可变剪接mapping和SNP分析的软件

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所属分类:Bioinformatics

基因组或者转录组数据的mapping中常用的软件有bwa、soap、tophat等等,其中tophat可以用于mapping存在可变剪接的reads。这里给大家介绍一款中山大学开发的一款可以用于做可变剪接分析的软件,MapNextMapNext可以mapping既可以mapping存在可变剪接的也可以mapping不存在可变剪接的reads,此外还可以做SNP检测以及SNP频率分析。

下面是其网站上的简短介绍:

MapNext provides four mainly analysis: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcriptomic reads, (iii) SNP detection and calculation of SNP frequency from population sequences, and (iv) storage of result data into database to make it available for more flexible query and further analyses.

MapNext下载,请访问软件的官方网站:http://evolution.sysu.edu.cn/english/software/mapnext.htm

里面有关于软件的使用以及相关参数的介绍,特别是其软件的manual,写得很详细。点击这里直接阅读MapNext使用手册说明manual_mapnext.pdf

下面是其软件的论文摘要和全文链接:

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

Hua Bao, Yuanyan Xiong, Hui Guo, Renchao Zhou, Xuemei Lu, Zhen Yang, Yang Zhong and Suhua Shi

Background

Next-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcript reads onto a reference genome and estimate minor allele frequency from sequences of population samples.

Results

We have designed and implemented MapNext, a software tool for both spliced and unspliced alignments of short sequence reads onto reference sequences, and automated SNP detection using neighbourhood quality standards. MapNext provides four main analyses: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcript reads over intron boundaries, (iii) SNP detection and estimation of minor allele frequency from population sequences, and (iv) storage of result data in a database to make it available for more flexible queries and for further analyses. The software tool has been tested using both simulated and real data.

Conclusion

MapNext is a comprehensive and powerful tool for both spliced and unspliced alignments of short reads and automated SNP detection from population sequences. The simplicity, flexibility and efficiency of MapNext makes it a valuable tool for transcriptomic and population genomic research.

全文地址:http://www.biomedcentral.com/1471-2164/10/S3/S13

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    来自外部的引用: 1

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