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galru 1.0.0

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)