Altools: a user friendly NGS data analyser.BACKGROUND
 Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions.  Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations.


 Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations.  Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms.  Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of positive predictive values, sensitivity, the identification of large deletion breakpoints and copy number detection.


 Altools is fast, reliable and easy to use for the mining of NGS data. 
Altools
Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. 
BWA/SAMtools/VarScan pipeline
Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. 
dnaCopy algorithm
A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. 
BLASTn