Description

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

fastq (file)

fastq file(s)

*.{fastq,fq}{.gz}

fasta (file)

fasta file

*.{fa,fna}

db_point (directory)

database directory containing known point mutations

db_res (directory)

database directory containing known resistance genes

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

json (file)

CGE standardized json file

*.json

disinfinder_kma (directory)

directory holding kma results

disinfinder_kma

pheno_table_species (file)

table with species specific AMR phenotypes

pheno_table_species.tsv

pheno_table (file)

table with all AMR phenotypes

pheno_table.tsv

pointfinder_kma (directory)

directory holding kma results

pointfinder_kma

pointfinder_prediction (file)

tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected

PointFinder_prediction.txt

pointfinder_results (file)

tab separated table with predicted point mutations leading to antibiotic resistance

PointFinder_results.txt

pointfinder_table (file)

predicted point mutations grouped into genes to which they belong

PointFinder_table.txt

resfinder_blast (directory)

directory holding blast results

resfinder_kma

resfinder_hit_in_genome_seq (file)

fasta sequence of resistance gene hits found in the input data (query)

ResFinder_Hit_in_genome_seq.fsa

resfinder_kma (directory)

directory holding kma results

resfinder_kma

resfinder_resistance_gene_seq (file)

fasta sequence of resistance gene hits found in the database (reference)

ResFinder_Resistance_gene_seq.fsa

resfinder_results_table (file)

predicted resistance genes grouped by antibiotic class

ResFinder_results_table.txt

resfinder_results_tab (file)

tab separated table with predicted resistance genes

ResFinder_results_tab.txt

resfinder_results (file)

predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes

ResFinder_results.txt

versions (file)

File containing software versions

versions.yml
maintainer
Github user marrip
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