ariba_run

Tags: fastq local-assembly antimicrobial-resistance virulence ariba sample-scope

Identify genes by local assembly of reads.

Uses ARIBA (Antimicrobial Resistance Identification By Assembly) to detect AMR and virulence genes by creating local assemblies from paired-end reads.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2) where each read slot is Path

Inputs

record (
    meta: Record,
    r1: Path,
    r2: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path	Illumina R1 reads (paired-end)
r2	Path	Illumina R2 reads (paired-end)

db: Path

Name	Type	Description
db	Path	An ARIBA prepared database

Outputs

record (
    meta: Record,
    report: Path,
    summary: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
report	Path	Tab-delimited detailed report of gene detection results
summary	Path	Comma-separated condensed summary of detected genes
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Ariba Run Parameters

Parameter	Type	Default	Description
--ariba_db	string		A database to query, if unavailable it will be downloaded to the path given by --datasets_cache (choices: argannot, card, ncbi, megares, plasmidfinder, resfinder, srst2_argannot, vfdb_core, vfdb_full, virulencefinder)
--ariba_nucmer_min_id	integer	90	Minimum alignment identity (delta-filter -i)
--ariba_nucmer_min_len	integer	20	Minimum alignment identity (delta-filter -i)
--ariba_nucmer_breaklen	integer	200	Value to use for -breaklen when running nucmer
--ariba_assembly_cov	integer	50	Target read coverage when sampling reads for assembly
--ariba_min_scaff_depth	integer	10	Minimum number of read pairs needed as evidence for scaffold link between two contigs
--ariba_spades_options	string		Extra options to pass to Spades assembler
--ariba_assembled_threshold	number	0.95	If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set
--ariba_gene_nt_extend	integer	30	Max number of nucleotides to extend ends of gene matches to look for start/stop codons
--ariba_unique_threshold	number	0.03	If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set
--ariba_no_clean	boolean		Do not clean up intermediate files created by Ariba.

Used By

Subworkflows

• ariba - Rapidly identify genes by creating local assemblies from paired-end reads.

Workflows

• ariba - Gene identification through local assemblies.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• Ariba
  Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 3, e000131 (2017)

Source

View source on GitHub

Version

ARIBA_RUN:
    - ariba: 2.14.7