Galaxy |

fargene (version 0.1+galaxy1)

Input type:

Select 'paired end' reads or 'sequence' for genomes/contigs

Forward reads (R1):

The file of forward reads in FASTQ format

Reverse reads (R2):

The file of reverse reads in FASTQ format

Resistance Genes:

The threshold score for a sequence to be classified as a (almost) complete gene:

The threshold score for a fragment to be classified as a positive. Expressed as score per amino acid:

Rescue short unassmebled plasmids:

The minimal length for a retrieved predicted ORF (nt):

Use this flag if the whole sequence where a hit is detected should be retrieved:

Do not perform ORF prediction:

Use if no quality control should be performed on the metagenomic data:

Use if you want to skip the assembly and retrieval of contigs for metagenomic data:

Use NCBI ORFfinder instead of prodigal for ORF prediction of genomes/contigs:

Store the translated sequences:

Useful if you plan to redo the analysis using a different model and want to skip the preprocessing steps

fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. The tool includes developed and optimized models for a number or resistance gene types, and the functionality to create and optimize models of your own choice of resistance genes.

The current version of the tool includes developed and optimized models for identification of the following resistance genes

Class A beta-lactamases

Subclass B1 and B2 beta-lactamases

Subclass B3 beta-lactamases

Class C beta-lactamases

Class D beta-lactamases

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