galru 1.0.0

galru: CRISPR types

Galru

Contents

• Introduction
• Installation
  • Ubuntu/Debian
  • Docker
• Usage
• License
• Feedback/Issues
• Citation

Introduction

Galru allows for rapid spoligotyping for Mycobacterium tuberculosis directly from long read sequencing. It is fast and accurate. It requires a minimal amount of information to produce a spoligotype, and allows for near real-time typing when used to process sequencing data as it is produced by a Nanopore sequencer.

Installation

If you just want to quickly try out the software please try a Docker continer. This software is designed to run on Linux and OSX. It will not run on Windows.

Conda

To install Galru, first install conda with Python3 then run:

conda install -c conda-forge -c bioconda galru

Docker

Install Docker. There is a docker container which gets automatically built from the latest version of Galru. To install it:

docker pull quadraminstitute/galru

To use it you would use a command such as this (substituting in your filename/directories), using the example file in this repository:

docker run --rm -it -v /path/to/example_data:/example_data quadraminstitute/galru galru /example_data/example_reads.fastq

Usage

Quick start

galru

usage: galru [options] uncorrected_long_reads.fastq

Spoligotyping from uncorrected long reads

positional arguments:
  input_file            Input FASTQ file of uncorrected long reads (optionally gzipped)

optional arguments:
  -h, --help            show this help message and exit
  --db_dir DB_DIR, -d DB_DIR
                        Base directory for species databases, defaults to bundled (default: None)
  --cas_fasta CAS_FASTA, -c CAS_FASTA
                        Cas gene FASTA file (optionally gzipped), defaults to bundled (default: None)
  --technology {map-ont,map-pb,ava-pb,ava-ont}, -y {map-ont,map-pb,ava-pb,ava-ont}
                        Sequencing technology (default: map-ont)
  --threads THREADS, -t THREADS
                        No. of threads to use (default: 1)
  --output_file OUTPUT_FILE, -o OUTPUT_FILE
                        Output filename, defaults to STDOUT (default: None)
  --extended_results, -x
                        Output extended results (default: False)
  --gene_start_offset GENE_START_OFFSET, -g GENE_START_OFFSET
                        Only count CRISPR reads which cover this base (default: 30)
  --min_mapping_quality MIN_MAPPING_QUALITY, -m MIN_MAPPING_QUALITY
                        Minimum mapping quality score (default: 10)
  --qcov_margin QCOV_MARGIN, -q QCOV_MARGIN
                        Maximum perc coverage difference between CRISPR and read (default: 100)
  --min_bitscore MIN_BITSCORE, -b MIN_BITSCORE
                        Minimum blast bitscore (default: 38)
  --min_identity MIN_IDENTITY, -i MIN_IDENTITY
                        Minimum blast identity (default: 95)
  --species SPECIES, -s SPECIES
                        Species name, use galru_species to see all available (default: Mycobacterium_tuberculosis)
  --debug               Turn on debugging and save intermediate files (default: False)
  --verbose, -v         Turn on verbose output (default: False)
  --version             show program's version number and exit

License

Galru is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues or to provide feedback please go to the issues page. If you make improvements to the software, add databases or extend profiles, please send us the changes though a pull request so that the whole community may benefit from your work.

Citation

Coming soon

Etymology

galrú (Gal-roo) is the word for infection in Irish (Gaeilge).

External Dependencies

System

• grep
• xargs
• find
• gunzip

Conda

• cd-hit-est (from cd-hit)
• minced
• bedtools
• samtools (1.3 or above)
• minimap2
• ncbi-genome-download
• blast+

Pypi

• fastaq (from pyfastaq)