Indigo

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

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Trace & basecall viewer

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Alt1 Alignment

Alt2 Alignment

Alt1 vs Alt2 Alignment

Variants

Decomposition plot

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Application Description

Indigo is a rapid SNV and InDel discovery method for Chromatogram traces obtained from Sanger sequencing of PCR products. The tool can separate a mutated and wildtype allele with the help of a provided reference. Indigo aligns both alleles against the reference genome, calls variants and annotates these variants with rs identifiers. Indigo also estimates the allelic fractions based on the mixed traces.

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 selected from the dropdown menu, an uploaded fasta file (*.fa) or another trace file (*.scf, *.abi, *.ab1, *.ab! and *.ab).

Sample Data

The "Show Example" button loads an example trace file (click to download file) that is then separated into two alleles. Both alleles are aligned to the reference, variants are called and annotated and results can be downloaded in PDF and VCF format.