bwa-mem2 VS IntaRNA

Compare bwa-mem2 vs IntaRNA and see what are their differences.

bwa-mem2

The next version of bwa-mem (by bwa-mem2)
Bioinformatics Genomics sequence-alignment
Source Code
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IntaRNA

Efficient target prediction incorporating accessibility of interaction sites (by BackofenLab)
Bioinformatics Interaction rna Structure Tool
Source Code
backofenlab.github.io
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bwa-mem2 IntaRNA
2 1
676 44
1.8% -
2.6 6.6
4 months ago 3 months ago
C++ C++
GNU General Public License v3.0 or later GNU General Public License v3.0 or later
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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

Posts with mentions or reviews of bwa-mem2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-06-28.
  • Anyone use DRAGEN-GATK?
    1 project | /r/bioinformatics | 12 Oct 2022
    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
    2 projects | /r/bioinformatics | 28 Jun 2022
    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

IntaRNA

Posts with mentions or reviews of IntaRNA. We have used some of these posts to build our list of alternatives and similar projects.
  • IntaRNA optimization
    1 project | /r/bioinformatics | 31 Mar 2023
    There might be, the code is open source (https://github.com/BackofenLab/IntaRNA/) so just download it, and run it through a code profiler, see where most of the runtime is spend and optimise the code.

What are some alternatives?

When comparing bwa-mem2 and IntaRNA you can also consider the following projects:

minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences

salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

bowtie2 - A fast and sensitive gapped read aligner

minimap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences

algo-ds-101 - algo-ds-101

htslib - C library for high-throughput sequencing data formats

Node-and-express-structure-using-cpp

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

seq - A high-performance, Pythonic language for bioinformatics

vg - tools for working with genome variation graphs

fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

bwa-mem2 vs minimap2 IntaRNA vs salmon bwa-mem2 vs bowtie2 IntaRNA vs bowtie2 bwa-mem2 vs minimap2 IntaRNA vs algo-ds-101 bwa-mem2 vs htslib IntaRNA vs Node-and-express-structure-using-cpp bwa-mem2 vs edlib IntaRNA vs seq bwa-mem2 vs vg IntaRNA vs fastp