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
maintainer
Github user louperelo
get in touch
Ask a question on Slack Open an issue on GitHub

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