Gencore is an efficient bioinformatics tool developed by HaploX for removing redundant sequencing information. It can provide fast, memory-efficient PCR duplicate removal and consensus read generation for NGS data with or without UMIs, with informative statistical reports to facilitate quality control and downstream analysis.

PCR duplicates are sequence reads resulting from sequencing multiple PCR copies of the same DNA fragment. They are removed by most analysis pipelines as they may contain PCR errors contributing to false-positive mutations. However, most existing bioinformatics tools for PCR duplicate removal either cannot handle UMI-barcoded data or are slow, memory-intensive and lack statistical results reporting that informs quality control and downstream analysis.

Gencore was published in December 2019 in BMC Bioinformatics and is available as an open-source tool on GitHub.

MutScan is a high-performance bioinformatics tool for the detection and visualization of target mutations. It is designed to improve detection sensitivity and offer efficient validation for target mutations.

In contrast to conventional multi-step mutation detection pipeline, MutScan can directly detect target mutations from raw FASTQ files using a string searching algorithm with high error tolerance to increase sensitivity. MutScan can then validate the detected mutations, or mutations identified by conventional pipelines, via an HTML report for each mutation, from which users can evaluate the confidence of a mutation via multiple metrics, such as the number of supporting reads, the quality scores of the bases at a mutation point and the rate of duplicated reads.

MutScan was published in BMC Bioinformatics in January 2018 and is available as an open-source tool on GitHub.

FineMSI is HaploX's novel, patented bioinformatics tool for analyzing microsatellite loci and determining MSI status.

It evaluates the earth movers' distance (EMD), a mathematical method to evaluate dissimilarity, between the distributions of MSI-high data and MSI-low data, with the EMD value signifying the degree of MSI.

FineMSI can interrogate substantially more informative microsatellite loci than existing gold standard methods. In in-house validation studies, FineMSI demonstrated greater sensitivity and specificity than a widely used NGS-based MSI method, indicating the potential of FineMSI as an accurate method for MSI status determination.