Indigo

InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products.

Get help · Source

Trace & basecall viewer

Plot help: Zoom/pan/hover Toolbar

Alt1 Alignment

Alt2 Alignment

Alt1 vs Alt2 Alignment

Variants

Decomposition plot

Plot help: Zoom/pan/hover Toolbar

Application Description

Indigo is a tool to deconvolute sanger trace files with the help of a provided reference. Indigo calculates the sequence of two allels based on the mixed traces read sequencing both allels at the same time with one primer.

Accepted Input

The trace files can be provided in abi or scf trace format (*.scf, *.abi, *.ab1, *.ab! and *.ab). The reference can be a genome selecte from the dropdown menu, an uploaded as a fasta file (*.fa) or a other trace file (*.scf, *.abi, *.ab1, *.ab! and *.ab).

Sample Data

The "Show Example" button loads an sample trace file (click to download file) and aligns it to a sample reference fasta file (click to download file).