Indigo is a rapid single-nucleotide variant (SNV) and insertion/deletion (InDel) discovery method in Chromatogram traces obtained from Sanger sequencing of PCR products. It can separate a mutated and wildtype allele and aligns both alleles against a reference sequence or wildtype chromatogram. Indigo discovers mutations generated by genome editing tools such as CRISPR/Cas9 or TALENs.

Indigo can be run online as a web application at https://www.gear-genomics.com/indigo.