edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. (by Martinsos)

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edlib discussion

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edlib reviews and mentions

Posts with mentions or reviews of edlib. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-01-03.
  • What's an efficient way to find multiple subsequences in several FASTQs?
    1 project | /r/bioinformatics | 8 Feb 2022
    I’ve got a similar situation. I was implementing the Smith-Waterman algorithm when I figured someone had to have already written a “fast” version of this. I found the edlib package (https://github.com/Martinsos/edlib) which does sequence alignment using Levenshtein distance. Essentially same DP algorithm as your traditional NW or SW only this is a C++ implementation with a Python wrapper. (I’m assuming you’re using Python, could be wrong though). The pertinent aspects of the output of this function contains the distance (dissimilarity) and the location (what index does the alignment start and end). This tool may go a ways to helping your pipeline. You could also look to metagenomic papers for inspiration as this is a problem (find a substring in a huge amount of data) that the community contends with all the time. Kmer based approach may also be useful if you want to attempt the alignment free path. Cheers.
  • ModuleNotFoundError after running `pip install -e .` locally
    2 projects | /r/learnpython | 3 Jan 2022
    I appear to get that error with the original source as well. https://github.com/Martinsos/edlib

Stats

Basic edlib repo stats
2
484
1.1
about 1 year ago

Martinsos/edlib is an open source project licensed under MIT License which is an OSI approved license.

The primary programming language of edlib is C++.


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