edlib
nanopolish
| edlib | nanopolish | |
|---|---|---|
| 2 | 1 | |
| 484 | 541 | |
| - | - | |
| 1.1 | 5.2 | |
| about 1 year ago | 9 months ago | |
| C++ | C++ | |
| MIT License | MIT License |
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edlib
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What's an efficient way to find multiple subsequences in several FASTQs?
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.
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ModuleNotFoundError after running `pip install -e .` locally
I appear to get that error with the original source as well. https://github.com/Martinsos/edlib
nanopolish
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ONT Frustration
I use nanopore for de novo methylation motif detection and some ssDNA signal comparison. Tombo has not worked with R10 data for me, so I’ll have to revisit that. Nanocompore uses Nanopolish for signal comparison, which does not support R10 data (see github).
What are some alternatives?
seq - A high-performance, Pythonic language for bioinformatics
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
bwa-mem2 - The next version of bwa-mem
bowtie - An ultrafast memory-efficient short read aligner
libnitrokey - Communicate with Nitrokey devices in a clean and easy manner
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
casadi - CasADi is a symbolic framework for numeric optimization implementing automatic differentiation in forward and reverse modes on sparse matrix-valued computational graphs. It supports self-contained C-code generation and interfaces state-of-the-art codes such as SUNDIALS, IPOPT etc. It can be used from C++, Python or Matlab/Octave.
opensim-core - SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
frugally-deep - Header-only library for using Keras (TensorFlow) models in C++.
stellarium - Stellarium is a free GPL software which renders realistic skies in real time with OpenGL. It is available for Linux/Unix, Windows and macOS. With Stellarium, you really see what you can see with your eyes, binoculars or a small telescope.
edlibtest - Private changes to https://github.com/Martinsos/edlib