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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

log (file)

log file

*.{log}

txt (file)

analysis summary text file

*.{txt}

hmm (file)

output from hmmsearch

*.{out}

orfs (file)

open reading frames (ORFs)

*.{fasta}

orfs_amino (file)

protein translation of open reading frames (ORFs)

*.{fasta}

contigs (file)

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

*.{fasta}

contigs_pept (file)

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

*.{fasta}

filtered (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 (file)

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

*.{fasta}

fragments (file)

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

*.{fastq}

trimmed (file)

The quality controlled retrieved fragments from each input file.

*.{fasta}

spades (directory)

The output from the SPAdes assembly

spades_assembly

metagenome (file)

The FASTQ to FASTA converted input files from metagenomic reads.

*.{fasta}

tmp (file)

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

*.{fasta}
included in
funcscan
author
Github user louperelo
get in touch
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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