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Quick Start

This guide walks you through your first in-silico PCR run with Amplirust.

Prerequisites

Install Amplirust using one of the methods from the Installation page:

conda install bioconda::amplirust

Step 1: Prepare Input

You need a sequence file (FASTA or GenBank) and a primer pair. For this example, we'll search for 16S rRNA using universal primers.

Create a primer CSV file primers.csv:

name,forward,reverse
16S,AGAGTTTGATCMTGGCTCAG,TACGGYTACCTTGTTACGACTT

Or pass the primer directly on the command line:

-p "16S:AGAGTTTGATCMTGGCTCAG:TACGGYTACCTTGTTACGACTT"

Step 2: Run Your First PCR

amplirust \
  -i genome.fasta \
  -p primers.csv \
  -o products.fasta \
  --tsv stats.tsv

Step 3: Understand the Output

Amplirust produces two outputs:

FASTA file (products.fasta) -- extracted PCR product sequences:

>genome_1:16S:1 pos=100-1600    strand=+    len=1501
AGAGTTTGATCATGGCTCAG...

TSV file (stats.tsv) -- detailed match statistics including primer positions, edit distances, identity scores, and CIGAR strings.

Summary printed to stderr:

=== Amplirust Summary ===
Input sequences:  1
Primer pairs:     1
Products found:   1

Next Steps