title: MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China. baohua@mail2.sysu.edu.cn
authors: Hua
authors: H
authors: Bao
authors: Yuanyan
authors: Y
authors: Xiong
authors: Hui
authors: H
authors: Guo
authors: Renchao
authors: R
authors: Zhou
authors: Xuemei
authors: X
authors: Lu
authors: Zhen
authors: Z
authors: Yang
authors: Yang
authors: Y
authors: Zhong
authors: Suhua
authors: S
authors: Shi
mesh_terms: D000483:Alleles; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012985:Software Design