bowtie2
A fast and sensitive gapped read aligner (by BenLangmead)
IntaRNA
Efficient target prediction incorporating accessibility of interaction sites (by BackofenLab)
Our great sponsors
| bowtie2 | IntaRNA | |
|---|---|---|
| 2 | 1 | |
| 619 | 44 | |
| - | - | |
| 7.4 | 6.6 | |
| 4 days ago | 3 months ago | |
| C++ | C++ | |
| GNU General Public License v3.0 only | 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.
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.
bowtie2
Posts with mentions or reviews of bowtie2.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-09-14.
-
NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).
- Computationally intensive steps in RNA-seq analysis
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
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 bowtie2 and IntaRNA you can also consider the following projects:
STAR - RNA-seq aligner
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
bwa-mem2 - The next version of bwa-mem
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
algo-ds-101 - algo-ds-101
seq - A high-performance, Pythonic language for bioinformatics
Node-and-express-structure-using-cpp
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
kraken2 - The second version of the Kraken taxonomic sequence classification system