sprog

Species Probes Generator - scripts to generate probe sequences for species identification.

The idea is you provide a set of genomes and their species names, a taxonomy for the species, and sprog can make a set of sequence probes that are unique to each node in the tree.

sprog was developed to generate Mycobacterium probes for mykrobe. However, the method is not specific to mykrobe and can be used more generally for any species.

The method relies heavily on Bifrost. Unitigs are generated from a graph of all the input genomes. Then the presence of these unitigs in each species is determined (where there is more than one genome for a species, a unitig must be found in all the genomes to be assigned to that species). This presence information is combined with the taxonomy to produce a set of sequences that are unique to node in the tree, in FASTA format.

Installation

sprog is written in Python. It assumes Bifrost is installed and in your $PATH.

Install sprog by taking a copy of this repo and running:

python3 -m pip install .

Optional dependencies:

• datasets - this is the command line tool from NCBI. You can either provide sprog with your own FASTA files, in which case datasets is not required. Alternatively, provide genbank or assembly accessions. datasets is used to download assemblies (genbank sequences are downloaded using wget)
• mash
• fastANI

If mash and/or fastANI are installed, then you can use the sprog commands mash_all/fastani_all to run all genomes vs all genomes using these tools. This is not required to build probes, but may be useful for sanity checking. It can help identify species where a genome has a better match to a different species.

Usage

This section is under construction.

For generating mykrobe probes, please see the section below.

Synopsis for making mykrobe probes

The following commands can be used to make mykrobe species probes for use with mykrobe predict and species tb. It is split over several scripts because the memory and multi-cpu usage varies significantly between stages.

Download data from GTDB (<100M RAM, a few minutes run time)

sprog mykrobe_from_gtdb GTDB_data

Download genomes (<100M RAM, approx 30 minutes to run depending on bandwidth)

sprog get_data Samples GTDB_data/manifest.tsv

Build graph of all samples and extract unitigs (17GB RAM, 1h wall clock)

sprog build_all_samples_unitigs --threads 30 Samples

Assign unitigs to each species (3GB RAM, 6h wall clock)

sprog per_sample_presence --threads 30 Samples

Make mykrobe probes (3GB RAM, 20m run time)

sprog make_probes --mykrobe_tb Samples GTDB_data/tree.tsv