A strain resolver for metagenomics.
cargo install lorikeet-rs
Not implemented yet
git clone https://github.com/rhysnewell/Lorikeet/git && cd Lorikeet && cargo build --release
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
Genotype will produce multiple .fna files representative of the expected strain level genotypes
Polymorph produces a tab delimited file containing possible variants and their positions within the reference
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.