andrija997 / bwt

Project from the course of Genom informatics at ETF Belgrade, Burrows Wheeler Transformation

This is a GitHub repo containting novice implementation of BWT and FM index lookup.
Project is tested on string lookup using Big Data genoms abailable at: https://ftp.ncbi.nlm.nih.gov/genomes/
Youtube video (in Serbian) explaining BWT and results of project: https://www.youtube.com/watch?v=OH0kSHD_uno&ab_channel=ivamil

To start this code you'll need to have access to special files containting sorted BW matrix or create your own one (using rotation_with_indices function -> This is the case when rotation matrix can't fit memory).

Command line exec assumes that you have all files needed in 'Data/';

Arguments needed:
1. File name which contains sequnce eg. "13443_ref_Cara_1.0_chr1c.fa"
2. Sequence for lookup eg. "CCTG"
3. Suffix array offset eg. 1, 4, 16, 64 or 254
4. Tally matrix offset eg. 1, 8, 32, 128 or 512

bwt's Issues

Write Readme.md

With explanations on how to run and what the tool does.

Add links

Add a link to the repo to youtube video description and link to YT video to Readme.md.

Add input file name as cmd line parameter

...instead of having it hardcoded. That way the script can be used from cmd line environment.

Remove commented code no longer used

Remove Serbian comments since the most of the comments are in English

Remove # In[31]: comments