Galaxy |

DeepARG short reads (version 1.0.4+galaxy0)

hide_db_build:

Forward mate from paired end library:

Reverse mate from paired end library:

DeepARG database:

Minimum identity for ARG alignments:

default value is 80

Minimum probability for considering a reads as ARG-like:

default value is 0.8

Minimum e-value for ARG alignments:

default value is 1e-10

Minimum coverage required for considering a full gene in percentage:

This parameter looks at the full gene and all hits that align to the gene. If the overlap of all hits is below the threshold the gene is discarded. Use with caution, default value is 1

minimum identity a read as a 16s rRNA gene:

default value is 0.8

Selection of the output files

Selection of the output files 0

The DeepARG Short Reads Pipeline is a specialized tool for detecting antibiotic resistance genes (ARGs) directly from paired-end short read sequencing data

It provides detailed output files summarizing ARG detection, merged results, subtype and type classifications, potential ARGs, and all detected hits

If you want to annotate ARGs from assembled contigs, use the DeepARG Predict tool