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_fargene

${task.process}

:string

The name of the process

fargene

:string

The name of the tool

0.1

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

fargene

:string

The name of the tool

0.1

:string

The expression to obtain the version of the tool

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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