Read Origin Protocol

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.

Written by:

• Serghei Mangul (smangul@ucla.edu)
• Kevin Hsieh (kevin.hsieh@ucla.edu)
• Linus Chen (u6.30cl@gmail.com)
• Harry Taegyun Yang (harry2416@gmail.com)

at the University of California, Los Angeles (UCLA).

Released under the terms of the General Public License, version 3.0 (GPLv3). For more information, please visit: https://github.com/smangul1/rop/wiki

Installing ROP

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.

Using ROP

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!