NGSTools

The NGSTools package provides an object model to enable different types of analyses of Next Generation Sequencing (NGS) data, and some utility programs to process reads aligned to different reference genomes. The most important tools in this package are SNVQ, an accurate Single Nucleotide Variants (SNV) detection and genotyping Algorithm from base calls and quality scores and a rule set to merge read alignments to a CCDS transcripts library with alignments of the same reads to a reference Assembly. The format of choice to process alignments in every tool in this package is SAM, which allows to integrate NGSTools with commonly used mapping programs as Bowtie and other Analysis packages like SAMTools