Amplicon Analyzer

Run setup

Start with defaults, then tune assay-specific settings as needed.

single or multi-site

Run name

Site name

Reference amplicon sequence

Use A/C/G/T/N bases. Reads are evaluated in forward and reverse-complement orientations.

Setting CSV

Imports the Amplicon Analyzer setting template. Blank fields are ignored during assay inference.

Assay type

The reference is the full expected PCR amplicon. Exact target bases are highlighted from the target-position field.

Target positions, 1-based amplicon coordinates

Low-depth warning threshold

Additional sites (optional)

Rows use: site name, reference amplicon, target positions. Additional sites use custom target positions.

FASTQ files

R1/R2 files are grouped by inferred sample name.

0 files

Drop FASTQ files here Supports FASTQ, FASTQ.GZ, and joined FASTQ text files

Processing

For large files, validate the run with a modest read limit before scaling up.

ready

Minimum mean Q

Minimum read length

Read limit per sample

Leave blank or enter 0 to process every read.

Minimum alignment identity (%)

Reads below this identity are excluded from mutation calling.

First sample number

Last sample number

Expected sample count

Optional filename filter for numbered samples. Files without a number are skipped while this filter is active.

Edit signal shown in heatmap

Expected base edit

Used for expected-edit summaries and exports; it does not change alignment.

Exclude reads containing N bases

Add FASTQ files, then run the analysis.

Preflight

Review inferred setup before running the analysis.

needs files

Export

Figure exports use the displayed site; table and summary exports include all sites.

waiting

Run log

Processing status and recoverable warnings appear here.

Samples0FASTQ sample groups

Alignment-passed reads0Reads passing identity threshold

Median depth0Alignment-passed reads per sample

Max edit %0.0selected signal

Warnings0QC / alignment warnings

Mutation heatmap

Add FASTQ files or load example data to generate a figure.

Displayed site

Load FASTQ files to generate the figure

Confirm the reference sequence, add FASTQ files, then click Run analysis.