Normalized compression distance for alignment-free biological sequence comparison
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README.md

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snacc: compress and compare pathogen genomes without sequence alignment

snacc is a pipeline that implements the normalized compression distance (NCD) specifically for biological data. The workflow primarily consists of 3 stages: compression, clustering, and visualization. The goal of this project is to provide a faster method of comparing large-scale pathogen genomes to conventional alignment-based methods such as BLAST by exploiting the inherent redundancies of the genetic code.

Table of contents

Workflow

workflow

Installation and Dependencies

Set up a virtual env (optional)

To install virtualenv use the following command in your terminal:

pip install virtualenv

Then in the directory you want to use, create a virtualenv named env:

virtualenv -p python3.6 env

And then activate the environment with:

source env/bin/activate

You can leave the virtualenv at any time with the command:

deactivate

Install the dependencies

To install the dependencies:

pip install git+https://github.com/SweetiePi/snacc

Optional: install BWT disk functionality

To use snacc with the BWT-Disk function you can run the following commands:

cd /path/to/snacc/bin/bwt_disk
make clean
make

Examples

  1. Before calling snacc
source activate my_env
  1. Most basic usage
snacc -d [folder with sequences] -o [output name]
  1. Intermediate: customize number of threads and compression algorithm
snacc -d [folder with sequences] -o [output name] -n 24 -c gzip
  1. Full control
snacc \
--directory [folder with sequences] \
--output [output name] \
--num-threads 24 \
--compression zlib \
--save-compression [folder to store zipped files] \
--show-progress False

Using bwt-disk functionality

The following command will run a burrows-wheeler transform in disk using the default amount of memory (256MB) and then compress using range encoding.

snacc\
--directory [folder with sequences] \
--output [output name] \
--num-threads 24 \
--compression bwt-disk \
--bwte-compress rle-range-encoding
--save-compression [folder to store zipped files] \
--show-progress False

Output

snacc analysis

  • Analysis time: 2018-10-14 15:18:17.257619
  • Analysis duration: 0:00:26.383997
  • Compression method: lzma
  • Reverse complement: False
  • Burrows-Wheeler transform: False
  • Output filepath: /Users/BenjaminLee/Desktop/Python/Research/hackseq18/bioncd-hackseq/test.csv
Analyzed Files
  • /Users/BenjaminLee/Desktop/Python/Research/hackseq18/bioncd-hackseq/test_dataset/mysteryGenome_1.fasta
  • /Users/BenjaminLee/Desktop/Python/Research/hackseq18/bioncd-hackseq/test_dataset/mysteryGenome_2.fasta
Distance Matrix
file mysteryGenome_1.fasta mysteryGenome_2.fasta
mysteryGenome_1.fasta 0.000644 0.003542
mysteryGenome_2.fasta 0.003542 0.000641
Version Information
  • Python: 3.6.0 (v3.6.0:41df79263a11, Dec 22 2016, 17:23:13) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
  • snacc: 0.0.1
  • scikit-learn: 0.20.0
  • py-lz4framed: 0.12.0
  • umap-learn: 0.3.5

results