Running Analyses

Running Analyses

insilicoPCR can analyze genome assemblies and sequencing reads.

Supported inputs

Supported sequence inputs include:

• .fasta
• .fa
• .fna
• .fastq
• .fq

The input can be a single file or a directory containing multiple sequence files.

Standard PCR analysis

Use a primer FASTA where each assay has:

• one -F forward primer
• one -R reverse primer

Example:

>targetA-F
ATGCGTACGTTAGCTAGCTA
>targetA-R
TCGATCGATACGCGTACGTA

qPCR/probe analysis

Use a primer FASTA where each assay has:

• one -F forward primer
• one -R reverse primer
• one -P probe

Example:

>targetB-F
GCTAGCTAGGATCGATCGAA
>targetB-R
TTCGATCGATCCTAGCTAGC
>targetB-P
ACGTTAGCTAGCTACGTA

Do not mix PCR modes

Do not mix assays with probes and assays without probes in the same primer FASTA file.

If any assay includes a -P probe, the consolidated report runs in qPCR mode and requires probe support for positive reporting.

Parameters

Parameter	Purpose
Threads	Number of worker threads
Mismatches	Allowed primer mismatches
E-value	BLASTN e-value threshold

Outputs

Outputs vary by run, but typically include logs, detailed report files, consolidated reports, and files used by the synthetic gel visualizer.