Lorikeet: A Rust repository from wwood

Introduction

Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short read datasets. Lorikeet combines short read variant calling with Freebayes and long read structural variant calling with SVIM to generate a complete variant landscape present across samples within a microbial community. SNV are also linked together using read information to help provide likely genotypes based on observed physical linkages.

Installation

Option 1: Conda - Recommended

Install into current conda environment:

conda install lorikeet-genome

Create fresh conda environment and install lorikeet there:

conda create -n lorikeet -c bioconda lorikeet-genome && \
conda activate lorikeet

Option 2: Cargo

conda create -n lorikeet -y -c conda-forge -c bioconda -c defaults -y parallel pysam=0.16 svim \ 
freebayes=1.3.2 prokka samtools bcftools vt rust clangdev pkg-config zlib gsl starcode openblas bwa minimap2 \ 
fastani dashing r-base && \ 
conda activate lorikeet && \ 
cargo install lorikeet-genome

Option 3: Build manually

You may need to manually set the paths for C_INCLUDE_PATH, LIBRARY_PATH, LIBCLANG_PATH, and OPENSSL_DIR to their corresponding paths in the your conda environment if they can't properly be found on your system.

conda create -n lorikeet -y -c conda-forge -c bioconda -c defaults -y parallel pysam=0.16 svim \ 
freebayes=1.3.2 prokka samtools bcftools vt rust clangdev pkg-config zlib gsl starcode openblas bwa minimap2 \ 
fastani dashing r-base && \ 
conda activate lorikeet && \ 
git clone https://github.com/rhysnewell/Lorikeet/git && \ 
cd Lorikeet && \ 
bash build.sh

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
    polymorph   Calculate variants along contig positions
    summarize   Summarizes contig stats from multiple samples
    evolve  Calculate dN/dS values for genes from read mappings

Less used utility subcommands:
    kmer    Calculate kmer frequencies within contigs
    filter    Remove (or only keep) alignments with insufficient identity

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

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

Genotype from bam:

lorikeet genotype -b input.bam -r input_genome.fna --e-min 0.1 --e-max 0.5 --pts-min 0.1 --pts-max 0.5

Genotype from short reads and longread bam:

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

Workflow

Output

Genotype

Genotype will produce multiple .fna files representative of the expected strain level genotypes

Polymorph

Polymorph produces a tab delimited file containing possible variants and their positions within the reference

Evolve

Evolve will produce dN/dS values within coding regions based on the possible variants found along the reference. These dN/dS values only take single nucleotide polymorphisms into account but INDELs can still be reported.

Summarize

Produce a SNP summary report for each contig in the provided MAG

wwood/Lorikeet