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 .fasta
--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