SequencEnG (Sequencing Techniques Engine for Genomics) is an educational resource for interactive learning of next-generation sequencing (NGS) techniques.
RACKJ (Read Analysis & Comparison Kit in Java) is a set of Java programs that analyze and compare RNA-seq data made by NGS (Next-Generation Sequencing) technologies. In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
NGS-MC is an R package which calculates the statistics and estimators in a Markov sequence model including the effective coverage, a chi-square statistic for k-words, normal approximation for every k-word, and five estimators for the order of Markov chain from NGS short read data.
mirTrios was developed for identification and comprehensive analysis the de novo and rare inherited variants with one or multiple trios samples based on high-throughput sequencing data starting from a VCF file (version 4). It uses reference gene definitions and hg19 genomic coordinates for annotation.
Nesoni is a high-throughput sequencing data analysis toolset, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced.
Pathoscope takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.
Clinical Pathoscope is a program to identify pathogens/commensals/contaminants in unassembled sequencing reads.
BM-Map is a powerful NGS genomic loci mapping refiner. It improves the mapping of the multireads (reads mapped to more than one genomic location with similar fidelities), as a refinement step after the general read-alignment is completed.
