Command-line reference

The command hierarchy is:

smfprimer design {sequence,fasta,annotated,bed,tss} [options]

Run smfprimer design MODE --help for the authoritative option list and defaults installed with your version.

Shared design options

Option	Meaning
--workflow {deaminase,conversion}	Experimental conversion model
--converted-strand {top,bottom}	Reference strand subjected to conversion
--context {cpg,gpc,both}	Protected cytosine context
--min-length, --optimum-length, --max-length	Primer3 size constraints
--min-tm, --optimum-tm, --max-tm	Primer3 Tm constraints
--min-gc, --max-gc	GC fractions from 0 to 1
--search-window N	Bases searched on each side of the target
--product-size MIN:MAX	Complete amplicon-size range
--max-results N	Maximum ranked pairs per target
--max-degeneracies N	Maximum degenerate (Y/R) bases tolerated per primer (default: 3)
--format {tsv,json}	Tabular output format
--output PATH	Write table rather than standard output
--genbank-output PATH	Override companion GenBank path
--no-genbank	Disable companion GenBank output
--bowtie-index PREFIX	Enable Bowtie 1 specificity

Input-specific options

Sequence

smfprimer design sequence SEQUENCE_OR_FASTA \
  --target-start START --target-end END

--target-id controls the result name.

FASTA

smfprimer design fasta LOCI.fa --target-width N [--gtf FEATURES.gtf.gz]

Annotated

smfprimer design annotated CONSTRUCT.gb \
  [--required-feature LABEL] \
  [--required-features-file NAMES.txt]

BED

smfprimer design bed --genome GENOME.fa --bed TARGETS.bed [--gtf FEATURES.gtf.gz]

TSS

smfprimer design tss \
  --genome GENOME.fa --gtf FEATURES.gtf --genes GENES.txt \
  [--tss-upstream N] [--tss-downstream N] \
  [--tss-policy {all,longest}]