bigglab / BIGGDATA

Immune Repertoire Analysis Portal

BIGGDATA

BIGGDATA is a web portal for analyzing IG and TCR repertoire data, originally built for the Brent Iverson George Georgiou (BIGG) Laboratory.

The goal of this system is twofold: to curate and provide a central repository for sequencing data collected by the lab, and to standardize analysis of IG and TCR repertoire data.

Users are able to import data from local files, server files, NCBI SRA, web URLs or UT Austin GSAF sequencing core directories, preprocess sequencing data (quality & illumina adapter trimming, quality filtering, paired-end overlap consensus) and run a variety of analysis programs (MixCR, IGFFT, Abstar, etc) to annotate reads from IMGT and native databases. Paired VH::VL (or TRB::TRA) sequencing analysis is now supported as well.

All annotation results are standardized to facilitate downstrem analysis and generate useful insights into repertoire distribution, polarization, and loci & gene usage. Comparative analysis of results between sample datasets includes a variety of repertoire similarity metrics and co-clustering to determine clonal overlap.

Installation

Dependencies:

python2.7 w/ Flask

rabbitmq-server

PostgreSQL Database

Celery task executor

Other python modules listed in requirements.txt

Programs utilized:

Trimmomatic

fastx_toolkit

Pandaseq

MiXCR

IGFFT

AbSTAR

Custom installation options can be made by modifying the instance/config.py file

Execution

Start Broker

rabbitmq-server

Start Celery

testing: celery -A app.celery worker --loglevel=debug

production: celery multi restart node1 --verbose -A app.celery --loglevel=info

Start Celery Admin (if you want to monitor task progression)

flower --port=8001

Start Web Service

python manage.py runserver -p 8000 -h 0.0.0.0

Check It Out At http://0.0.0.0:8000

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Installation Instructions To Come