merlin

Tags: species-specific automated mash minmer typing bactopia-tool

MinMER-assisted species-specific tool selection and execution.

This Bactopia Tool, Merlin, uses MinMER distances based on the RefSeq sketch to automatically run species-specific analysis tools. Merlin identifies the closest reference genomes and executes appropriate typing and analysis tools for each detected species.

Usage

Bactopia CLI:

bactopia --wf merlin \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/merlin/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       ├── clermontyping
│       │   ├── <SAMPLE_NAME>.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       ├── <SAMPLE_NAME>.blast.xml
│       │       ├── <SAMPLE_NAME>.html
│       │       └── <SAMPLE_NAME>.mash.tsv
│       ├── ectyper
│       │   ├── <SAMPLE_NAME>.blast_alleles.txt
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── ectyper.log
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── kleborate
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── merlindist
│       │   └── merlin-<TIMESTAMP>
│       │       ├── <SAMPLE_NAME>-dist.txt
│       │       └── logs
│       │           ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │           └── versions.yml
│       ├── shigapass
│       │   ├── <SAMPLE_NAME>.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       └── ShigaPass_summary.csv
│       ├── shigatyper
│       │   ├── <SAMPLE_NAME>-hits.tsv
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── shigeifinder
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       └── stecfinder
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
├── <SAMPLE_NAME>SE
│   └── tools
│       ├── clermontyping
│       │   ├── <SAMPLE_NAME>SE.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       ├── <SAMPLE_NAME>SE.blast.xml
│       │       ├── <SAMPLE_NAME>SE.html
│       │       └── <SAMPLE_NAME>SE.mash.tsv
│       ├── ectyper
│       │   ├── <SAMPLE_NAME>SE.blast_alleles.txt
│       │   ├── <SAMPLE_NAME>SE.tsv
│       │   └── logs
│       │       ├── ectyper.log
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── kleborate
│       │   ├── <SAMPLE_NAME>SE.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── merlindist
│       │   └── merlin-<TIMESTAMP>
│       │       ├── <SAMPLE_NAME>SE-dist.txt
│       │       └── logs
│       │           ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │           └── versions.yml
│       ├── shigapass
│       │   ├── <SAMPLE_NAME>SE.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       └── ShigaPass_summary.csv
│       ├── shigatyper
│       │   ├── <SAMPLE_NAME>SE-hits.tsv
│       │   ├── <SAMPLE_NAME>SE.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── shigeifinder
│       │   ├── <SAMPLE_NAME>SE.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       └── stecfinder
│           ├── <SAMPLE_NAME>SE.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
├── SRR13039589
│   └── tools
│       ├── clermontyping
│       │   ├── SRR13039589.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       ├── SRR13039589.blast.xml
│       │       ├── SRR13039589.html
│       │       └── SRR13039589.mash.tsv
│       ├── ectyper
│       │   ├── SRR13039589.blast_alleles.txt
│       │   ├── SRR13039589.tsv
│       │   └── logs
│       │       ├── ectyper.log
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── kleborate
│       │   ├── SRR13039589.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── merlindist
│       │   └── merlin-<TIMESTAMP>
│       │       ├── SRR13039589-dist.txt
│       │       └── logs
│       │           ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │           └── versions.yml
│       ├── shigapass
│       │   ├── SRR13039589.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       └── ShigaPass_summary.csv
│       ├── shigatyper
│       │   ├── SRR13039589-hits.tsv
│       │   ├── SRR13039589.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── shigeifinder
│       │   ├── SRR13039589.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       └── stecfinder
│           ├── SRR13039589.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── merlin-<TIMESTAMP>
        ├── merged-results
        │   ├── clermontyping.tsv
        │   ├── ectyper.tsv
        │   ├── kleborate.tsv
        │   ├── logs
        │   │   ├── clermontyping-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── ectyper-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── kleborate-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── shigapass-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── shigatyper-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── shigeifinder-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   └── stecfinder-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   ├── shigapass.tsv
        │   ├── shigatyper.tsv
        │   ├── shigeifinder.tsv
        │   └── stecfinder.tsv
        └── nf-reports
            ├── merlin-dag.dot
            ├── merlin-report.html
            └── merlin-timeline.html

Species-Specific Analysis

note

Tools executed depend on detected species

File	Description
Analysis	results from all executed species-specific tools

Merged Results

File	Description
merlin.tsv	Merged summary of all species-specific analyses

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
merlin-dag.dot	The Nextflow DAG visualization
merlin-report.html	The Nextflow Execution Report
merlin-timeline.html	The Nextflow Timeline Report
merlin-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Type	Default	Description
--bactopia	string		The path to bactopia results to use as inputs

mashdist Parameters

Parameter	Type	Default	Description
--mash_sketch	string		The reference sequence as a Mash Sketch (.msh file)
--full_merlin	boolean	false	Go full Merlin and run all species-specific tools, no matter the Mash distance

ClermonTyping Parameters

Parameter	Type	Default	Description
--clermontyping_threshold	integer	0	Do not use contigs under this size

ECTyper Parameters

Parameter	Type	Default	Description
--ectyper_opid	integer	90	Percent identity required for an O antigen allele match
--ectyper_opcov	integer	90	Minimum percent coverage required for an O antigen allele match
--ectyper_hpid	integer	95	Percent identity required for an H antigen allele match
--ectyper_hpcov	integer	50	Minimum percent coverage required for an H antigen allele match

emmtyper Parameters

Parameter	Type	Default	Description
--emmtyper_wf	string	blast	Workflow for emmtyper to use. (choices: blast, pcr)
--emmtyper_blastdb	string		Path to custom EMM BLAST DB.
--emmtyper_cluster_distance	integer	500	Distance between cluster of matches to consider as different clusters
--emmtyper_percid	integer	95	Minimal percent identity of sequence

hicap Parameters

Parameter	Type	Default	Description
--hicap_gene_coverage	number	0.8	Minimum percentage coverage to consider a single gene complete
--hicap_gene_identity	number	0.7	Minimum percentage identity to consider a single gene complete
--hicap_broken_gene_length	integer	60	Minimum length to consider a broken gene
--hicap_broken_gene_identity	number	0.8	Minimum percentage identity to consider a broken gene

Mykrobe Parameters

Parameter	Type	Default	Description
--mykrobe_species	string		Species panel to use (choices: sonnei, staph, tb, typhi)
--mykrobe_opts	string		Extra Mykrobe options in quotes

GenoTyphi Parameters

Parameter	Type	Default	Description
--genotyphi_mykrobe_opts	string		Extra Mykrobe options in quotes

Kleborate Parameters

Parameter	Type	Default	Description
--kleborate_preset	string	kpsc	Preset module to use for Kleborate (choices: kpsc, kosc, escherichia)
--kleborate_opts	string		Extra options in quotes for Kleborate

legsta Parameters

Parameter	Type	Default	Description
--legsta_noheader	boolean	false	Don't print header row

LisSero Parameters

Parameter	Type	Default	Description
--lissero_min_id	number	95.0	Minimum percent identity to accept a match
--lissero_min_cov	number	95.0	Minimum coverage of the gene to accept a match

ngmaster Parameters

Parameter	Type	Default	Description
--ngmaster_csv	boolean	false	output comma-separated format (CSV) rather than tab-separated

pasty Parameters

Parameter	Type	Default	Description
--pasty_min_pident	integer	95	Minimum percent identity to count a hit
--pasty_min_coverage	integer	95	Minimum percent coverage to count a hit

pbptyper Parameters

Parameter	Type	Default	Description
--pbptyper_min_pident	integer	95	Minimum percent identity to count a hit
--pbptyper_min_coverage	integer	95	Minimum percent coverage to count a hit

SeqSero2 Parameters

Parameter	Type	Default	Description
--seqsero2_run_mode	string	k	Workflow to run. 'a' allele mode, or 'k' k-mer mode (choices: a, k)
--seqsero2_input_type	string	assembly	Input format to analyze. 'assembly' or 'fastq' (choices: assembly, fastq)

SeroBA Parameters

Parameter	Type	Default	Description
--seroba_coverage	integer	20	Threshold for k-mer coverage of the reference sequence

SISTR Parameters

Parameter	Type	Default	Description
--sistr_full_cgmlst	boolean	false	Use the full set of cgMLST alleles which can include highly similar alleles

AgrVATE Parameters

Parameter	Type	Default	Description
--agrvate_typing_only	boolean	false	agr typing only. Skips agr operon extraction and frameshift detection

spaTyper Parameters

Parameter	Type	Default	Description
--spatyper_do_enrich	boolean	false	Do PCR product enrichment

sccmec Parameters

Parameter	Type	Default	Description
--sccmec_min_targets_pident	integer	90	Minimum percent identity to count a target hit
--sccmec_min_targets_coverage	integer	80	Minimum percent coverage to count a target hit
--sccmec_min_regions_pident	integer	85	Minimum percent identity to count a region hit
--sccmec_min_regions_coverage	integer	93	Minimum percent coverage to count a region hit

STECFinder Parameters

Parameter	Type	Default	Description
--stecfinder_use_reads	boolean	false	Paired-end Illumina reads will be used instead of assemblies
--stecfinder_hits	boolean	false	Show detailed gene search results
--stecfinder_cutoff	number	10.0	Minimum read coverage for gene to be called
--stecfinder_length	number	50.0	Percentage of gene length needed for positive call

TB-Profiler Profile Parameters

Parameter	Type	Default	Description
--tbprofiler_call_whole_genome	boolean	false	Call whole genome
--tbprofiler_mapper	string	bwa	Mapping tool to use. If you are using nanopore data it will default to minimap2 (choices: bwa, minimap2, bowtie2, bwa-mem2)
--tbprofiler_caller	string	freebayes	Variant calling tool to use (choices: bcftools, gatk, freebayes)
--tbprofiler_opts	string		Extra options in quotes for TBProfiler

TB-Profiler Collate Parameters

Parameter	Type	Default	Description
--tbprofiler_itol	boolean	false	Generate itol config files
--tbprofiler_full	boolean	false	Output mutations in main result file
--tbprofiler_all_variants	boolean	false	Output all variants in variant matrix
--tbprofiler_mark_missing	boolean	false	An asterisk will be used to mark predictions which are affected by missing data at a drug resistance position

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Type	Default	Description
--include	string		A text file containing sample names (one per line) to include from the analysis
--exclude	string		A text file containing sample names (one per line) to exclude from the analysis

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• bactopia_datasets - Download and provide pre-compiled datasets required by Bactopia.
• merlin - MinER assisted species-specific bactopia tool seLectIoN.

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)

• Mash
  Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016)

Source

View source on GitHub