lorikeet-rs

A strain resolver for metagenomics.

Installation

option 1: Cargo

cargo install lorikeet-rs

option 2: Conda

Not implemented yet

option 3: Build manually

git clone https://github.com/rhysnewell/Lorikeet/git && cd Lorikeet && cargo build --release

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 reads:

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

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.