seq
edlib
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| seq | edlib | |
|---|---|---|
| 15 | 2 | |
| 634 | 484 | |
| - | - | |
| 0.7 | 1.1 | |
| over 1 year ago | about 1 year ago | |
| C++ | C++ | |
| Apache License 2.0 | MIT License |
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seq
- Bioinformatics programming language
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A Python-based programming language for high-performance computational genomics
> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications
- Seq – A programming language for computational genomics and bioinformatics
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Hacker News top posts: Sep 15, 2021
Seq: A programming language for high-performance computational genomics\ (17 comments)
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Seq: A programming language for high-performance computational genomics
They support both, and will deprecate Python 2 style soon.
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
What are some alternatives?
Nim - Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula. Its design focuses on efficiency, expressiveness, and elegance (in that order of priority).
bwa-mem2 - The next version of bwa-mem
adam - ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
nanopolish - Signal-level algorithms for MinION data
wyng-backup - Fast Time Machine-like backups for logical volumes & disk images
libnitrokey - Communicate with Nitrokey devices in a clean and easy manner
Biopython - Official git repository for Biopython (originally converted from CVS)
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.
bowtie2 - A fast and sensitive gapped read aligner
frugally-deep - Header-only library for using Keras (TensorFlow) models in C++.
seq-genomics - Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang
edlibtest - Private changes to https://github.com/Martinsos/edlib