GATACA is developing novel algorithms and software solutions for virologists. Funded by several Small Business Innovation Research (SBIR) awards from the NSF and NIH (NIAID), our current focus is on the hepatitis B virus (HBV) bioinformatics. We have developed an algorithm for assembling deep coverage NGS data using a novel contig merge-refine-cluster iteration approach for retaining all suspected true variants, resolving haplotypes and characterizing quasispecies. Our pipeline for the hepatitis C virus (HCV) incorporates resistance profiling and mutation tracking/variant calling algorithms directly from NGS reads.
Baseline quality controls allow removal of unwanted reads (e.g., too short, low quality bases); error correction, extraction of redundant and contaminating reads (e.g., microbial, human). The resulting dataset includes only the viral data, thus streamlining down-stream analytics.
Resolving quasispecies composition is a daunting challenge in viral informatics. Our proprietary assembly algorithm utilizes an iterative scheme to produce contigs and interconnections highly representative of intra-host variation, including long-range and in the low frequency realm. Alignments enable comparison of output to our dynamic databases with up-to-date resistance mutations, including DAAs.
Key protein coding regions are critical to understanding the specifics of viral structure and mutation potential. Our methods automatically segregate and identify these regions with unprecidented rapidity.
Implementing a dynamic design has enabled us to overcome the challenges associated with static database design; our databases are scalable and flexible, require minimal data reconstruction, and are updated regularly with emerging variant information (resistance, replacement, escape, etc).
The key to a solid data management system is integrating the workflow, such as attaching annotations to sequences, creating data linkages, extracting sequence-specific features for simplifying and unifying your data input with automation; discerning batch effects and meaningful offsets, and unmasking hidden patterns and trends can be ascertained by integrating the results of multiple experiments with proper normalization and cross-compiling.
The Forum for Collaborative Research
HHS Viral Hepatitis Action Plan
Center for the Study of Hepatitis C
Center for Innovative Technology
Strategies and algorithms custom designed for small complex genomes.
Our team of skilled writers and field-matched bioinformatics experts will advise on the strategy, structure, and creation of your scientific documents and presentation materials. Our team can help you maximize the impact of your work by creating clear, concise, and powerful publication- and presentation-ready material. Services are offered at varying levels to match individual needs and a work plan will be created to match.
Our team has extensive experience working with, educating, and advocating along-side priority populations identified in the Viral Hepatitis Action Plan. We are available and interested in partnering with research teams looking to advance the Action Plan by decreasing health disparities through education, awareness, and improved access to care.