Biological Repository (BioR) for Genomic Annotation

Overview:

BioR is light-weight annotation distribution infrastructure. It is a general purpose genomic data integration tool that enables genomic coordinate based or accession lookup searches. This user guide will help get you up to speed in how to use BioR. BioR utilizes catalogs, which are the data files containing the data of interest. Please see Installation Guide to get this tool for yourself.

Catalogs:

A BioR catalog is basically a BED-JSON hybrid file that is

indexed using Tabix for coordinate based search and BioR’s own indexing system for string matching based searches.

• Creating Catalogs
  • Indexing your Samples
  • Creating Custom Catalogs
  • Examples: Building Catalogs from tab-delimited data
  • Dots in Column Names (and JSON Keys):
  • Indexing the Data for Coordinate Based Search
  • Hints on Creating Indexes on Custom Catalogs
• Catalog Format Changes
  • 1.0.0 (2012-12)
  • 1.1.0 (2014?)
  • 1.1.1 (2017)
• Creating a Catalog in Seconds
• BioR Catalog Shortcut
• Finding out what is in a Catalog
  • BioR Commands
• Showin the Commands in BioR Toolkit

Toolkit:

BioR uses a Pipe-And-Filter architecture. Data to be annotated by BioR is streamed through a pipeline, a sequence of one or more pipes. Pipes is based on Flow Based Programming by J.P. Morrison. DataFlow-Article, Flow-Based-Programing.

Figure 1: BioRTools works by adding annotation to the right on the original file.

BioR leverages UNIX pipes to flow data from program to program. As BioR programs work on the data, they place annotation to the right (the red, blue and green columns in Figure 1).

• bior_build_catalog
• bior_drill
• Get all Variants in a Gene
• bior_modify_tjson
• Pretty Print
• bior_replace_lines
• bior_catalog_stats