amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence. (by ncbi)
hap.py
Haplotype VCF comparison tools (by Illumina)
| amr | hap.py | |
|---|---|---|
| 1 | 2 | |
| 242 | 395 | |
| 5.0% | 1.8% | |
| 7.1 | 0.0 | |
| 13 days ago | 6 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.
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
hap.py
Posts with mentions or reviews of hap.py.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Help running hap.py
I have been tasked with benchmarking a variant calling pipeline running hap.py as part of my bioinformatics MSc project.
- cream π
What are some alternatives?
When comparing amr and hap.py you can also consider the following projects:
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
GenomicSQLite - Genomics Extension for SQLite
seq - A high-performance, Pythonic language for bioinformatics
truvari - Structural variant toolkit for VCFs
gw - Genome browser and variant annotation
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.