bwa-mem2
edlib
Our great sponsors
| bwa-mem2 | edlib | |
|---|---|---|
| 2 | 2 | |
| 676 | 484 | |
| 1.8% | - | |
| 2.6 | 1.1 | |
| 4 months ago | about 1 year ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
bwa-mem2
-
Anyone use DRAGEN-GATK?
If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
-
Software Development Project
I’ve recently switched to bwa mem2 and the speed increase is nice for what is basically a drop in replacement (after a bit of validation to make sure that was true). https://github.com/bwa-mem2/bwa-mem2
edlib
-
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.
-
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?
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
seq - A high-performance, Pythonic language for bioinformatics
bowtie2 - A fast and sensitive gapped read aligner
nanopolish - Signal-level algorithms for MinION data
minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
libnitrokey - Communicate with Nitrokey devices in a clean and easy manner
htslib - C library for high-throughput sequencing data formats
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.
vg - tools for working with genome variation graphs
frugally-deep - Header-only library for using Keras (TensorFlow) models in C++.
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
edlibtest - Private changes to https://github.com/Martinsos/edlib