Commands
This page documents the available commands via the artic
command line interface.
basecaller
Overview
Display basecallers in files
Input
Output
Usage example
artic basecaller <directory>
demultiplex
Overview
Run demultiplex
Input
- undemultiplexed FASTA file
Output
- demultiplexed FASTA file(s)
Usage example
artic demultiplex <fasta>
Argument name(s) | Required | Default value | Description |
---|---|---|---|
fasta | Y | NA | The undemultiplexed FASTA file |
--threads | N | 8 | The number of threads |
--prefix | N | NA | Prefix for demultiplexed files |
--no-remove-directory | N | NA | Don't remove the directory |
export
Overview
The export command is used to make a redistributable package of data for re-analysis. This includes the FASTQ file, the sequencing summary and the FAST5 file. The selection of reads to be used comes from a BAM file, and only aligned reads are used.
Input
- a completed minion pipeline run
Output
- a redistributable package of data
Usage example
artic export <prefix> <bamfile> <sequencing_summary> <fast5_directory> <output_directory>
Argument name(s) | Required | Default value | Description |
---|---|---|---|
prefix | Y | NA | The run prefix |
bamfile | Y | NA | The BAM file to export reads from |
sequencing_summary | Y | NA | Path to Guppy sequencing summary |
fast5_directory | Y | NA | The path to directory of FAST5 files |
output_directory | Y | NA | The path to export the data to |
extract
Overview
Create an empty poredb database
Input
- na
Output
- an initialised poredb database
Usage example
artic extract <directory>
Argument name(s) | Required | Default value | Description |
---|---|---|---|
directory | Y | NA | The name of the database |
--basecalller | N | ONT Albacore Sequencing Software | The name of the basecaller |
filter
Overview
Filter FASTQ files by length
Input
- unfiltered reads
Output
- filtered reads
Usage example
artic filter --max-length 500 --min-length 50 <filename>
Argument name(s) | Required | Default value | Description |
---|---|---|---|
filename | Y | NA | The reads to filter |
--max-length | N | NA | Remove reads greater than max-length |
--min-length | N | NA | Remove reads less than than min-length |
gather
Overview
Gather up demultiplexed files
Input
- director[y/ies] to gather from
Output
- directory of gathered files
Usage example
artic gather --directory ./
Argument name(s) | Required | Default value | Description |
---|---|---|---|
--directory | Y | NA | The director[y/ies] to gather files from |
prefix | Y | NA | Prefix for gathered files |
--max-length | N | NA | Remove reads greater than max-length |
--min-length | N | NA | Remove reads less than than min-length |
--prompt-directory | N | NA | The run directory for interactive prompts |
--fast5-directory | N | NA | The directory with fast5 files |
--no-fast5s | N | NA | Do not use fast5s and nanopolish |
guppyplex
Overview
Aggregate pre-demultiplexed reads from MinKNOW/Guppy
Input
- director[y/ies] to aggregate from
Output
- directory of aggregated files
Usage example
artic guppyplex --directory ./
Argument name(s) | Required | Default value | Description |
---|---|---|---|
--directory | Y | NA | The director[y/ies] to gather files from |
prefix | Y | NA | Prefix for guppyplex files |
--max-length | N | NA | Remove reads greater than max-length |
--min-length | N | NA | Remove reads less than than min-length |
--quality quality | N | 7 | Remove reads against this quality filter |
--sample sample | N | 1 | Sampling frequency for random sample of sequence to reduce excess |
--skip-quality-check | N | NA | Do not filter on quality score (speeds up) |
minion
Overview
Run the alignment/variant-call/consensus pipeline
Input
- a primer scheme and a sample directory
Output
- trimmed alignments, variants calls and consensus sequence
Usage example
artic minion <scheme> <sample>
Argument name(s) | Required | Default value | Description |
---|---|---|---|
scheme | Y | NA | The name of the primer scheme |
sample | Y | NA | The name of the sample |
--medaka | N | False | Use medaka instead of nanopolish for variants |
--medaka-model | * | NA | Medaka model to use (required if --medaka set) |
--minimap2 | N | True | Use minimap2 |
--bwa | N | False | Use bwa instead of minimap2 |
--normalise | N | 100 | Normalise down to moderate coverage to save runtime |
--threads | N | 8 | Number of threads |
--scheme-directory | N | /artic/schemes | Default scheme directory |
--max-haplotypes | N | 1000000 | Max-haplotypes value for nanopolish |
--read-file | N | NA | Use alternative FASTA/FASTQ file to |
--fast5-directory | N | NA | FAST5 Directory |
--sequencing-summary | N | NA | Path to Guppy sequencing summary |
--skip-nanopolish | N | False | Skip nanopolish |
--no-longshot | N | False | Use medaka variant instead of longshot (experimental feautre from v1.2.0) |
--strict | N | False | Enables experimental features (from v1.2.0), including VFC overlap checks and stats |
--dry-run | N | False | Perform a dry run of the minion pipeline, outputing commands to a log but not executing them |
--medaka-model
is required if--medaka
is set.
rampart
Overview
Interactive prompts to start RAMPART
Input
Output
Usage example
run
Overview
Process an entire run folder interactively
Input
Output
Usage example