abricate
quast
abricate | quast | |
---|---|---|
3 | 1 | |
345 | 370 | |
- | 1.4% | |
0.0 | 0.0 | |
6 months ago | 9 months ago | |
Perl | AMPL | |
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
quast
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Deciding on genome assembly software
Have you looked into QUAST for comparison of assemblies? How big is the bacterial community? You may need to do some binning of your contigs to separate them into species specific genomes. I can suggest metaGEM (developed by me! should be online in NAR any day now) for generating MAGs for your bacterial species. Although it currently only supports short reads, it may give you an idea of what the bacterial community looks like. Maybe also look into EukCC for estimating fungal genome completeness and/or EukRep for splitting the contigs according to prokaryotic/eukaryotic provenance. You could also try estimating community composition directly from short read analysis using e.g. mOTUs2, kraken/braken, metaphlan, etc.
What are some alternatives?
ariba - Antimicrobial Resistance Identification By Assembly
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
abritamr - A pipeline for running AMRfinderPlus and collating results into functional classes
merqury - k-mer based assembly evaluation
MGEfinder - A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
CompareGenomeQualities - Reference free comparison of genome assemblies
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
clinker - Gene cluster comparison figure generator
DnaFeaturesViewer - :eye: Python library to plot DNA sequence features (e.g. from Genbank files)
EukCC - Tool to estimate genome quality of microbial eukaryotes