iris-av 1.0.1

IRIS: Detection and Validation Of Chimeric Reads

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

Requirement	Details
Language support	Python ≥ 3.6
Dependencies	-

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

Option	Description
-i1, --input1	Path to the file containing BLAST mapping of reads to genome 1. Alignment is expected to have the following format: -outfmt "6 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"
-i2, --input2	Path to the file containing BLAST mapping of reads to genome 2. Alignment is expected to have the following format: -outfmt "6 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"
-a1, --annotation1	Path to the file containing GTF/GFF annotation for genome 1.
-a2, --annotation2	Path to the file containing GTF/GFF annotation for genome 2.
-g1, --genome1	Path to the file containing genome 1 FASTA sequence.
-g2, --genome2	Path to the file containing genome 2 FASTA sequence.
--two-pass	Flag enables the 2-pass mode. Breakpoints from the first pass will be used to bias DP trace towards consensus sites.
--group	If enabled, will output a file with breakpoints groupped by position.
-o, --output	Path to the output file.
--chim-genome	(Requires -group). If enabled, will generate a fasta file with chimeric genome sequences, stitching together the two genomes at the breakpoints.
--max-dist	Maximum distance between breakpoints of the two segments. Default: 5.
---max-weight	Maximum weight of a breakpoint when biasing the 2nd pass. Default: 5.
--full-weight	Weight of a breakpoint that matches donor and acceptor. Default: 5.
--half-weight	Weight of a breakpoint that matches either donor or acceptor. Default: 3.
--overhang	Number of bases to include in the chimeric genome overhang. Default: 1000.

Help Options

Option	Description
-h, --help	Prints help message.

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