Read Origin Protocol

This project is no longer maintained as of January 2020 due to end-of-life for Python 2.

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from complex RNA molecules, recombinant antibodies, and microbial communities.

Created by Serghei Mangul, Kevin Hsieh, Linus Chen, and Harry Taegyun Yang at the University of California, Los Angeles (UCLA). Released under the terms of the General Public License, version 3.0 (GPLv3).

Installation

To install ROP, first clone this repository, then run

./install.sh

from the repository's directory. This will download dependencies and databases. The default installation will generally suffice, but the following options are available:

• -c|--clean: Just remove installed tools.
  • To reinstall, use -r|--reinstall instead.
  • Overrides conflicting options.
• -f|--force: Unlink databases.
  • Use with caution.
• -n|--native: Use native python.
  • MiniConda will not be downloaded.
  • You may use environment.yml to set up your python environment.
• -l|--link LINK: Link databases instead of downloading.
  • Useful if you previously downloaded an ROP database.
  • A symlink will be created in the current directory.
  • Overrides conflicting options.
• -d|--db-dest DB_DEST (default: .): Change database download location.
  • Useful for managing space.
  • A symlink will be created in the current directory.
• -o|--organism ORGANISM (default: human): Organism to download databases for.
  • Exactly one of the following: human, mouse.
• -r|--reinstall: Reinstall tools, even if they're already present.
• -s|--select-db SELECT_DB (default: all): Database(s) to download for the specified organism.
  • A comma-separated list of one or more of the following: basic, repeats, microbiome (which may be subdivided into metaphlan, viral, fungi, protozoa).
  • -s all selects everything.
• -h|--help: Displays usage information.

Usage

To use ROP, run

rop.sh unmapped_reads output_dir

Unless otherwise specified using an option, unmapped_reads must be a .fastq/.fq file, and output_dir must not exist (it will be created). Results will be written to output_dir, with one subdirectory for every stage of the pipeline. The following options are available:

• -o|--organism (default: human): Organism to run ROP for.
  • Exactly one of the following: human, mouse.
• -s|--steps (default: all except lowq): Select the analysis modes to use.
  • A comma-separated list of one or more of the following: lowq, rdna, reference, repeats, circrna, immune, microbiome (which may be subdivided into metaphlan, bacteria, viral, fungi, protozoa).
  • circrna and bacteria are not available in the current release.
  • -s all selects everything.
• -a|--fasta: Input unmapped reads in .fasta format instead of .fastq format. Forcibly disables low-quality read filtering.
• -b|--bam: Input unmapped reads in .bam format instead of .fastq format.
• -z|--gzip: gunzip the input file.
• -d|--dev: Keep intermediate FASTA files.
  • Consumes extra space.
• -f|--force: Overwrite the analysis destination directory.
• -i|--ignore-extensions: Ignore incorrect .fastq/.fq/.fasta/.fa file extensions. Does not ignore incorrect .gz/.bam file extensions.
• -m|--max: Use a liberal threshold when remapping to reference.
  • May account for more reads.
• -x|--commands: Print all commands (diagnostic mode).
• -h|--help: Displays usage information.

A small example file is included in the repository in various formats. To try it out, run one of the following commands from the repository directory:

rop.sh -b example/example.bam ropout
rop.sh example/example.fastq ropout
rop.sh -z example/example.fastq.gz ropout
rop.sh -a example/example.fasta ropout
rop.sh -az example/example.fasta.gz ropout

Then, browse to the ropout directory to see the analysis results!