Six functional prototypes available from the March NCBI hackathon


At the March 2017 NCBI Genomics Hackathon, participants developed six functional software prototypes, several of which are still under active development. Software is available from the NCBI-Hackathons GitHub site.

  1. Squidstream provides naming consistency by converting sequence feature IDs in entire files (bed, gff3, wig, etc.) to the desired ID format using a single command.
  2. ga4gh-ncbi-api is a method that links NCBI’s API and the GA4GH (Global Alliance for Genomics and Health) API, and generates a searchable list of genome datasets from NCBI.
  3. Graph_Extraction provides code to implement a simple graph genome browser.
  4. Sidearm searches the SRA database for viruses using the NCBI magicBLAST tool.
  5. Scan2CNV is a commandline tool that generates copy number variation (CNV) calls from raw SNP array data.
  6. Single Cell Reproducible Epigenomics Workflow (SCREW) is a single-cell whole-genome bisulfite sequencing (SC-WGBS) pipeline and docker image for performing standard single-cell DNA methylation analyses.
NCBI Hackathons Homepage

NCBI’s First Hackathon: Advanced Bioinformatic Analysis of Next-Gen Sequencing Data


This blog post is geared toward genomics professionals.

From January 5th-7th, 2015, NCBI, in conjunction with the NIH Office of Data Science, held a genomics hackathon, where genomics professionals gathered to write useful, efficient pipelines for people new to genomics.

After we announced the hackathon, over 130 qualified applicants expressed interest in attending. Four team leads chose 23 attendees from this pool, then assigned initial predefined roles and provided biological guidance for a product in one of four subject areas: DNA-Seq, RNA-Seq, Epigenomics and Metagenomics. Continue reading