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install with bioconda DOI

Lorikeet

Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially active regions within candidate genomes. Called variants can be clustered into likely strains using a combination of UMAP and HDBSCAN.

Documentation

For detailed documentation of Lorikeet and the various algorithms and concepts it touches on please visit the Lorikeet Docs

Quick Start

Installation

Lorikeet is distributed via Crates.io https://crates.io/crates/lorikeet-genome. Additional packages can be downloaded via conda using the lorikeet.yml file provided. Ensure that cargo is installed on your system:

curl https://sh.rustup.rs -sSf | sh

Then install lorikeet:

cargo install lorikeet-genome

Alongside required packages:

conda env create -f lorikeet.yml -n lorikeet
conda activate lorikeet

Usage

Input can either be reads and reference genome, or MAG. Or a BAM file and associated genome.

Strain genotyping analysis for metagenomics

Usage: lorikeet <subcommand> ...

Main subcommands:
    genotype    *Experimental* Resolve strain-level genotypes of MAGs from microbial communities
    consensus   Creates consensus genomes for each input reference and for each sample
    call        Performs variant calling with no downstream analysis
    evolve      Calculate dN/dS values for genes from read mappings

Other options:
    -V, --version   Print version information

Rhys J. P. Newell <r.newell near uq.edu.au>

Call variants from bam:

lorikeet call --bam-files my.bam --longread-bam-files my-longread.bam --genome-fasta-directory genomes/ -x fna --bam-file-cache-directory saved_bam_files --output-directory lorikeet_out/ --threads 10 --plot

Call variants from short reads and longread bam files:

lorikeet call -r input_genome.fna -1 forward_reads.fastq -2 reverse_reads.fastq -l longread.bam

Shell completion

Completion scripts for various shells e.g. BASH can be generated. For example, to install the bash completion script system-wide (this requires root privileges):

lorikeet shell-completion --output-file lorikeet --shell bash
mv lorikeet /etc/bash_completion.d/

It can also be installed into a user's home directory (root privileges not required):

lorikeet shell-completion --shell bash --output-file /dev/stdout >>~/.bash_completion

In both cases, to take effect, the terminal will likely need to be restarted. To test, type lorikeet ca and it should complete after pressing the TAB key.

License

Code is GPL-3.0