CLI Reference
amplirust [OPTIONS] --input <INPUT> --primers <PRIMERS>
| Option |
Default |
Description |
-i, --input <FILES> |
|
Input sequence files (comma-separated, glob patterns supported). Supports FASTA (.fasta, .fa, .fna, .ffn, .fas) and GenBank (.gb, .gbk, .gbff, .genbank, .gbf), including gzip-compressed (.gz). Unrecognized file types in glob results are skipped with a warning. |
-p, --primers <PRIMERS> |
|
Primers as name:forward:reverse or path to CSV file (with --pool: name:sequence) |
--circular |
false |
Treat sequences as circular genomes |
--max-decompression-size <N> |
4294967296 |
Maximum decompressed file size in bytes (0 = unlimited) |
Matching Options
| Option |
Default |
Description |
-k, --max-errors <N> |
2 |
Maximum edit distance for primer matching |
--min-identity <FLOAT> |
0 (disabled) |
Minimum identity threshold (0.0-1.0) |
--search-rc |
false |
Also search reverse complement strand |
-t, --threads <N> |
auto |
Number of threads (0 = auto-detect) |
Pool Options
| Option |
Default |
Description |
--pool |
false |
Treat primers as a pool of individual primers (all-vs-all matching) |
--pool-self-match |
false |
In pool mode, allow the same primer to match as both forward and reverse |
Product Options
| Option |
Default |
Description |
--min-len <N> |
50 |
Minimum PCR product length |
--max-len <N> |
5000 |
Maximum PCR product length |
--trim-primers |
false |
Remove primer sequences from output |
--max-n-fraction <F> |
0.1 |
Maximum fraction of N bases allowed in product sequence (0.0-1.0) |
Output Options
| Option |
Description |
-o, --output <FILE> |
Output FASTA file (.gz for compression) |
--tsv <FILE> |
TSV file with detailed statistics |
-v, --verbose |
Increase verbosity (-v, -vv, -vvv) |
-q, --quiet |
Suppress progress bar output |
--remove-duplicates |
Remove duplicate product sequences per reference (canonicalized by reverse complement) |
Progress Bar and Summary
Amplirust shows a progress bar while reading multiple input files (suppressed with --quiet or any -v flag). It always prints a run summary to stderr after processing.
⠋ [00:00:02] [########################################] 15/15 files (0s)
=== Amplirust Summary ===
Input sequences: 1250
Primer pairs: 3
Products found: 47
Products by primer:
16S: 45
ITS: 2
Products by reference:
genome_1: 30
genome_2: 17
Output written to: products.fasta
TSV written to: stats.tsv
Use --quiet to suppress the progress bar (useful for scripting). Progress bars are also disabled when any verbosity flag is set (-v, -vv, -vvv).