BinBencherBackend

BinBencherBackend.jl is a package for efficient benchmarking and interactive exploration of a set of metagenomic assembled genomes (MAGs) against a reference. This is designed to be used for benchmarking metagenomic binners against a simulated metagenome.

Installation

• Install Julia - preferably using juliaup: https://github.com/JuliaLang/juliaup
• Launch Julia: julia
• Press ] to enter package mode. You can exit package mode with backspace.
• In package mode, type add BinBencherBackend to download and install the benchmarking software

Quickstart

using BinBencherBackend
ref =  Reference("files/ref.json")
bins = Binning("files/clusters.tsv", ref)
print_matrix(bins)

Concepts

• A Sequence is a sequence (e.g. contig) clustered by the binner
• A Genome is a target genome that should be reconstructed by the binner. It can be a virus, organism, plasmid etc. Every Genome have several Sources, and one parent Clade.
• A Flag marks the certaincy about a boolean attribute of a genome, like "is this a virus?".
• Sources are the sequences that Genomes are composed of. These are typically the reference genome sequences originally obtained by assembly of a purified genome (e.g. clonal colony). Sequences map to zero or more Sources at particular spans, i.e. locations.
• A Clade contain one or more Genomes or Clades. Clades containing genomes are rank 1, and clades containing rank N clades are rank N+1 clades. All genomes descend from a chain of exactly N ranks of clades, where N > 0.
• A Bin is a set of Sequences created by the binner. Every bin is benchmarked against all genomes and clades in the reference.
• A Reference is composed of:
  • The genomes, a set of Genomes, each with a set of Sources and Flags
  • The taxmaps, a full set of Clades that encompasses every Genome at N ranks (where N > 0)
  • The sequences, a list of Sequences, each with zero or more mappings to Sources.
• A Binning is a set of Bins benchmarked against a Reference

See the Reference in the left sidebar.