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.

NCBI Hackathons Homepage

  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.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s