A rust classifier based on HNSW for prokaryotic genomes

ARCHAEA stands for: A Rust Classifier base on Hierarchical Navigable SW graphs, et.al.**

This package (currently in development) compute probminhash signature of bacteria and archaea genomes and stores the id of bacteria and probminhash signature in a Hnsw structure for searching of new request genomes.

This package is developped by Jean-Pierre Both (https://github.com/jean-pierreBoth) for the software part and Jianshu Zhao (https://github.com/jianshu93) for the genomics part.

Dependencies and Installation

• pre-compiled binaries are available in the release page for major platforms. For linux based system, no dependencies but system level gfortran must be later than gfortran@5, which means gcc 8.3 or above. If you want to compile from source, see below:

• Clone hnsw-rs and probminhash or get them from crate.io

  • git clone https://github.com/jean-pierreBoth/hnswlib-rs

  • git clone https://github.com/jean-pierreBoth/probminhash

• Clone kmerutils which is not in crate.io:

  • git clone https://github.com/jean-pierreBoth/kmerutils

• Clone ARCHAEA, which is not in crate.io:

  • git clone https://github.com/jean-pierreBoth/archaea

• Clone annembed:

  • git clone https://github.com/jean-pierreBoth/annembed annembed is now based on intel-mkl-static by default, to change to openblas you need to change "ndarray-linalg = {version = "0.14", features = ["intel-mkl-static"]}" to "ndarray-linalg = {version = "0.14", features = ["openblas-system"]}" in the Cargo.toml, if you do not have intel-mkl installed.

• Three libraries, zeromq, libsodium and openblas (optional for annembed_f feature) are required to successfully compile.

```bash

if you are using Linux (ubuntu for example), install them first

sudo apt-get install libzmq-dev libsodium-dev openblas

if you are using MacOS

brew install zeromq brew install libsodium

with MacOS monterey, BLAS are installed in the Architecture.framework, but you can still installed it and add library path to environmental variables according to homebrew promt message. See above annembed part to see how to use a different openblas in interl-mkl library

brew install openblas

cd archaea cargo build --release --features annembed_f

or, openblas library is not needed

cargo build --release

if you are using anaconda/miniconda3 or on a server, you can install them first, but remember to add library configuration path and dynamic library config path to you environmental variables. Openblas must be installed at system level for MacOS system (static link is not prefered by Apple). Ask your system manager to installed it for you.

we installed miniconda3 to the home directory

LIBZMQLIBDIR=~/miniconda3/lib LIBZMQINCLUDEDIR=~/miniconda3/include cargo build --release --features annembed_f

or without annembed feature, where openblas denpendency is not required

LIBZMQLIBDIR=~/miniconda3/lib LIBZMQINCLUDEDIR=~/miniconda3/include cargo build --release

```

• A dependency is provided as a feature. It uses the crate annembed that gives some statistics on the hnsw graph constructed (and will provide some visualization of data). It is activated by running:
  • cargo build --release --features annembed_f

Build on ARM64/aarch64, rust nightly version only

Nightly rust must be used ```bash

install rustup first, and the activate it

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

setup nightly rust

rustup default nightly

go to the kmerutils, annembed and archaea directory you just cloned, and change the line: hnswrs = {version = "0.1.15"} to hnswrs = {path = "../hnswlib-rs"} in both Cargo.toml

same processure with the above regular compiling.

```

Sketching of genomes

The sketching and database is done by the module tohnsw.

The sketching of reference genomes can take some time (one or 2 hours for 50000 bacterial genomes of NCBI for parameters giving a correct quality of sketching). Result is stored in 2 structures: - A Hnsw structure storing rank of data processed and corresponding sketches. - A Dictionary associating each rank to a fasta id and fasta filename.

The Hnsw structure is dumped in hnswdump.hnsw.graph and hnswdump.hnsw.data The Dictionary is dumped in a json file seqdict.json

Requests

For requests the module request is being used. It reloads the dumped files, hnsw and seqdict related takes a list of fasta files containing requests and for each fasta file dumps the asked number of nearest neighbours.

Classify

The classify module is used to assign taxonomy information from requested neighbours to query genomes. Average nucleitide identity will be calculated.

The last step involves a homology search using hmmer, which can be directly installed using conda or brew. If you are using apple M1 ARM/aarch64 structure. This is how you can have a native support of hmmer

```bash

download h3-heno branch of hmmer here (do not git clone but download zip):

https://github.com/EddyRivasLab/hmmer/tree/h3-arm

go into the donwloaded directory and download Easel develop branch here (do not git clone but download zip) :

cd h3-arm https://github.com/EddyRivasLab/easel/tree/develop

compile, or you can download binaries from here: https://github.com/jianshu93/hmmer-h3-arm

autoconf ./configure make -j 8 sudo make install hmmsearch -h ```

Usage

```bash

build database given genome file directory

tohnsw -d dbdirnt -s 12000 -k 21 --ef 1600 -n 128 tohnsw -d dbdiraa -s 24000 -k 7 --ef 1600 -n 128 --aa

request neighbours for each genomes in query_dir given pre-built database path

request -b ./ -d querydirnt -n 50 request -b ./ -d querydiraa -n 50 --aa ```

Pre-built databases

We provide pre-built genome/proteome database graph file for bacteria/archaea, virus and fungi. Proteome database are based on genes for each genome, predicted by prodigal (https://github.com/hyattpd/Prodigal) for bacteria/archaea/virus and GeneMark-ES version 2 (http://exon.gatech.edu/GeneMark/licensedownload.cgi) for fungi. Bacteria/archaea genomes are the newest version of GTDB database (https://gtdb.ecogenomic.org), which defines a bacterial speces at 95% ANI. Note that ARCHAEA can also run for even higher resolution species database such as 99% ANI. Virus data base are based on the JGI IMG/VR database newest version (https://genome.jgi.doe.gov/portal/IMGVR/IMG_VR.home.html), which also define a virus OTU (vOTU) at 95% ANI. Fungi database are based on the entire RefSeq fungal genomes, we dereplicated and define a fungal speices at 99% ANI. All three pre-built database can be available here: