bowtie
An ultrafast memory-efficient short read aligner (by BenLangmead)
amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence. (by ncbi)
| bowtie | amr | |
|---|---|---|
| 1 | 1 | |
| 267 | 370 | |
| 0.4% | 3.0% | |
| 10.0 | 5.9 | |
| about 4 years ago | 18 days 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.
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.
amr
Posts with mentions or reviews of amr.
We have used some of these posts to build our list of alternatives
and similar projects.
-
No antibiotic resistance genes in plasmidSPAdes assembly
https://github.com/ncbi/amr this tool will report the contig and coordinates for any AMR gene it detects in your assembly. If you want to know which genes are nearby you should also annotate your genome (with prokka for example) as the other response suggested
What are some alternatives?
When comparing bowtie and amr you can also consider the following projects:
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
octopus - Bayesian haplotype-based mutation calling
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
hap.py - Haplotype VCF comparison tools
nanopolish - Signal-level algorithms for MinION data
bowtie2 - A fast and sensitive gapped read aligner