README.md

Seq_Class

This repository contains a suffix tree based metagenomic classifier.

Installation

To install you must first have cargo and rustup installed:

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

After installing the above command you can run the following to install seq_class:

cargo install --git=https://github.com/sriram98v/seq_class

Alternatively, you can install seq_class by cloning this repository and building it locally:

git clone https://github.com/sriram98v/seq_class
cd seq-class
cargo install --path=./

Usage

In order to start classifying a set of reads, you need to build an index from you set of reference sequences. You can build an index using the following command.

seq_class build -s <reference sequence file path> -m <Maximum depth of index(use 5 if not sure)> -o <index file path> -n <number of reference sequences (0 for all)>

Once you have built an index, you can either query a single file with:

seq_class query -r <reads file> -p <percent mismatch> -t <index file>

or quey all the files in a directory:

seq_class query_dir -r <reads file> -p <percent mismatch> -t <index file> -o <output dir>

You can refer the man page for seq_class for more details by running

seq_class -h