abricate
ariba
abricate | ariba | |
---|---|---|
3 | 1 | |
342 | 155 | |
- | 0.6% | |
0.0 | 3.0 | |
5 months ago | 8 months ago | |
Perl | Python | |
GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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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
ariba
What are some alternatives?
abritamr - A pipeline for running AMRfinderPlus and collating results into functional classes
galaxy - Data intensive science for everyone.
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.