LINEBERGER BIOINFORMATICS CORE (LBC) NGS Informatics group
The NextGenSequencing (NGS) Informatics group manages data throughout its digital lifecycle. We handle the conversion of raw files from sequencers, download various data types from international repositories, develop and run computational workflows share results with local investigators and remote collaborators, and upload raw data to national and international repositories, and create web tools like jUNCtion which can manage datasets and run workflows,
Services
- jUNCtion. We develop, maintain, and administer jUNCtion, a web application that runs several standard workflows on managed datasets. The datasets may be generated locally at UNC’s Translational Genomics Laboratory (TGL), externally by the UNC High Throughput Sequencing Facility (HTSF), by remote collaborators, third-party vendors, or downloaded from major repositories. Among the workflows we support bulk DNA-seq, somatic variant calling of targeted and exome DNA (both paired-normal and tumor-only), RNA-seq expression, and several workflows using 10X Genomics single-cell analyses. Most workflows can process human or mouse sequencing data.
- Workflow development. In addition to developing the workflows used in jUNCtion, we create custom workflows based requests from local investigators. This includes modifying existing workflows for custom genomes or capture kits, adding new tools to our workflows, or completely new workflows. We primarily develop and run using Nextflow, which allows scalable and reproducible runs. We also troubleshoot workflows and containerize tools for reproducibility and portability. We can adapt third-party workflows and run off-the-shelf workflows. Occasionally, we also create and adapted algorithms into new tools.
- UNCseq. The UNCseq project’s sequencing data has been processed through our workflows and we can provide access to the both raw FASTQ data and the processed results. We periodically re-run phe data as our workflows evolve and improve.
- Data sharing. Working with Office of Genomics Research (OGR), we publish data to major repositories like EGA, dbGaP, and SRA. and download data from those and other repositories like TCGA. Data includes raw sequencing data, metadata, and can be public or private, with the latter sometimes requiring encryption or decryption, but in either case we conform to the requirements of the repositories and confirm accurate transport using checksums when appropriate. We also facilitate data sharing with collaborators using tools like Globus Connect, sftp, scp, and rsync.
Group Personnel
- Alan Hoyle: Bioinformatics Scientist, group manager.
Alan has been at UNC Lineberger since 2009 and developing computational workflows, debugging cluster and process issues, and automating data production processes. He has been managing the group since 2019. He has a background in computer science and has extensive experience developing databases and web applications. - Kan Liu: Bioinformatics Software Engineer
Kan joined UNC Lineberger in January of 2022 and designs, develops, and executes software to support advanced data analysis of LCCC-sponsored research, primarily through jUNCtion. He has a MS in Computer Science and 20 years of experience as a full stack software engineer. - Matthew Soloway: Bioinformatics Research Associate
Matt has been a member of UNC Lineberger since 2010. He collaborates with the Office of Genomics Research (OGR), to upload Lineberger data and metadata to various data repositories , downloads datasets, and facilitates bidirectional sharing with collaborators using various software tools. He also develops, tests, and automates in-house software to expedite our data-sharing processes. - David Marron: Bioinformatics Applications Specialist
David has been part of UNC Lineberger since 2015. He develops, maintains, and runs bioinformatics workflows and software, and also works on automation, testing, and research. He has an MS in computer science with a bioinformatics certificate. - Benjamin Wingo: Web Developer
Ben has been at UNC Lineberger since 2022 aiding in the development and support of the jUNCtion and LIMS web applications. He has a background in computer science with experience in Java full stack development.