ariba
abricate
| ariba | abricate | |
|---|---|---|
| 1 | 3 | |
| 154 | 337 | |
| 1.9% | - | |
| 3.0 | 0.0 | |
| 7 months ago | 5 months ago | |
| Python | Perl | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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ariba
abricate
- Predicting Antimicrobial Resistance in a Sequence
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best way to identify AMR genes from a whole genome
I personally use ABRicate because it's simple https://github.com/tseemann/abricate. But there's a whole heap of other tools and papers like this commenting on those https://www.frontiersin.org/articles/10.3389/fpubh.2019.00242/full
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best way to search whole genomes for known antibiotics resistance genes
Try abricate https://github.com/tseemann/abricate
What are some alternatives?
galaxy - Data intensive science for everyone.
abritamr - A pipeline for running AMRfinderPlus and collating results into functional classes
MGEfinder - A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
edgecase - A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.
16SMaRT - 16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).
hgvs - Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.