Description

tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input:file

uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)

*.{fasta}

hmm_model:string

name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]

Output

name:type
description
pattern

log

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.log:file

log file

*.{log}

txt

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/results_summary.txt:file

analysis summary text file

*.{txt}

hmm

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/hmmsearchresults/*.out:file

output from hmmsearch (both single gene annotations + contigs)

*.{out}

hmm_genes

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/hmmsearchresults/retrieved-*.out:file

output from hmmsearch (single gene annotations only)

retrieved-*.{out}

orfs

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/predictedGenes/predicted-orfs.fasta:file

open reading frames (ORFs)

*.{fasta}

orfs_amino

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/predictedGenes/predicted-orfs-amino.fasta:file

protein translation of open reading frames (ORFs)

*.{fasta}

contigs

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/predictedGenes/retrieved-contigs.fasta:file

(complete) contigs that passed the final full-length classification

*.{fasta}

contigs_pept

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/predictedGenes/retrieved-contigs-peptides.fasta:file

parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences

*.{fasta}

filtered

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/predictedGenes/*filtered.fasta:file

sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene

*.{fasta}

filtered_pept

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/predictedGenes/*filtered-peptides.fasta:file

sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located

*.{fasta}

fragments

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/retrievedFragments/all_retrieved_*.fastq:file

All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files

*.{fastq}

trimmed

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/retrievedFragments/trimmedReads/*.fasta:file

The quality controlled retrieved fragments from each input file.

*.{fasta}

spades

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/spades_assembly/*:directory

The output from the SPAdes assembly

spades_assembly

metagenome

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/tmpdir/*.fasta:file

The FASTQ to FASTA converted input files from metagenomic reads.

*.{fasta}

tmp

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}/tmpdir/*.out:file

The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option —store-peptides is used.

*.{fasta}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

fargene
MIT

Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output

github.com/fannyhb/fargene
included in
funcscan
maintainer
Github user louperelo
get in touch
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