bowtie
An ultrafast memory-efficient short read aligner (by BenLangmead)
bowtie2
A fast and sensitive gapped read aligner (by BenLangmead)
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| bowtie | bowtie2 | |
|---|---|---|
| 1 | 2 | |
| 252 | 615 | |
| - | - | |
| 10.0 | 7.6 | |
| almost 2 years ago | about 2 months ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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.
bowtie
Posts with mentions or reviews of bowtie.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-24.
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.
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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
What are some alternatives?
When comparing bowtie and bowtie2 you can also consider the following projects:
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
STAR - RNA-seq aligner
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
bwa-mem2 - The next version of bwa-mem
nanopolish - Signal-level algorithms for MinION data
seq - A high-performance, Pythonic language for bioinformatics
kraken2 - The second version of the Kraken taxonomic sequence classification system
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
CHM13 - The complete sequence of a human genome
vg - tools for working with genome variation graphs