amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence. (by ncbi)
bowtie2
A fast and sensitive gapped read aligner (by BenLangmead)
amr | bowtie2 | |
---|---|---|
1 | 2 | |
251 | 629 | |
6.4% | - | |
6.8 | 8.0 | |
8 days ago | 29 days 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.
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
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
What are some alternatives?
When comparing amr and bowtie2 you can also consider the following projects:
STAR - RNA-seq aligner
bwa-mem2 - The next version of bwa-mem
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
seq - A high-performance, Pythonic language for bioinformatics
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
IntaRNA - Efficient target prediction incorporating accessibility of interaction sites
kraken2 - The second version of the Kraken taxonomic sequence classification system
CHM13 - The complete sequence of a human genome
vg - tools for working with genome variation graphs