NGSTools – Java tools for analysis of Next Generation Sequencing (NGS) data
The NGSTools package provides an object model to enable different kinds of analysis 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 and HardMerge. SNVQ is an accurate Single Nucleotide Variants (SNV) detection and genotyping algorithm from base calls and quality scores. HardMerge merges alignments of a set of reads to two references (genome and transcriptome) given a set of rules that ensures confindently calling SNVs from the resulting set of alignments. 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.
NGSTools source code
Acknowledgment and Disclaimer
This material is based upon work supported in part by the National Science Foundation under Grants No. IIS-0546457 and IIS-0916948. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.