IRIS: Detection and Validation Of Chimeric Reads.

Introduction

IRIS is a method designed to detect and validate retroviral integration sites by analyzing RNAseq and/or DNAseq reads for signs of chimerism. The method constructs a DP alignment matrix from two separate alignments (host and pathogen) to infer precise breakpoint. The two-pass algorithm is implemented to refine consistency of breakpoint inference. The method is designed to take advantage of genomic anntoations of either or, ideally, both genomes involved in the chimeric event by penalizing and prioritizing events at known junctions.

Publications

Coming soon...

Documentation

Installation

Via PyPI

The easiest way to install IRIS is through PyPI:

$ pip install iris-av
$ iris --help

To uninstall SNAPPER:

$ pip uninstall iris-av

Building from source

To build from source, clone the git repository:

$ git clone https://github.com/alevar/iris.git --recursive
$ cd iris
$ pip install -r requirements.txt
$ pip install .

Requirements

Getting started

IRIS expects BLAST alignments to be provided in the following format:

blastn \
  -db blast_database \
  -query query_fasta \
  -out output.blastn6 \
  -outfmt "6 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"

Usage

iris [-h] -i1 INPUT1 -i2 INPUT2 -a1 ANNOTATION1 -a2 ANNOTATION2 -o OUTPUT [--two_pass] [-g] [--chim-genome]
                   [-g1 GENOME1] [-g2 GENOME2] [-max_dist MAX_DIST] [-max_weight MAX_WEIGHT]
                   [-full_weight FULL_WEIGHT] [-half_weight HALF_WEIGHT] [--overhang OVERHANG]

Options

Help Options

Example Data

Sample datasets are provided in the "example" directory to test and get familiar with SNAPPER.

The included example can be run with the following command from the root directory of the repository:

iris --input1 ./examples/AY69_E4p5_LTA/host.blastn.6 --input2 ./examples/AY69_E4p5_LTA/path.blastn.6 --annotation1 ./examples/AY69_E4p5_LTA/host.gtf --annotation2 ./examples/csess.1.0.0.known.gtf --output ./examples/AY69_E4p5_LTA/ris --genome1 ./examples/AY69_E4p5_LTA/host.fa --genome2 ./examples/SIV239.fa --chim-genome --two-pass --group