AmpUMI is a user-friendly software tool to assist in the design and the analysis of Unique molecular identifiers (UMIs) -based amplicon sequencing studies.
DAFGA estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene.
MetAmp tool is developed for analysis of amplicon data by combining several marker regions from 16S rRNA genes. Such marker regions serve as unique identificators for species.
PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.
ISME J. 2010 Jul;4(7):852-61. doi: 10.1038/ismej.2010.16. Epub 2010 Feb 25. PANGEA: pipeline for analysis of next generation amplicons.
Giongo A1, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW.
SESAME (SEquence Seeker and AMplicon Explorer)is a user friendly web application package for analyzing amplicon sequences obtained through NGS technologies. It was tested extensively with Mozilla Firefox 3.5 and Chrome web browsers. It is designed to provide individual amplicon alignments so the user(s) can easily validate alleles and distinguish them from sequencing errors and artifacts. It includes automatic sequence assignation to multiple loci and samples via oligonucleotides tags. An assistant guides the user for input data upload and through the automatic sequence analysis steps. It provides an intuitive point-and-click interface to validate sequences as alleles from amplicon sequences alignments. All data are stored in a relational database, that user can query or filter through an intuitive interface. The results are exported as genotypes or sequences of genetic variants.
Amplicon is a tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form. This is especially useful for designing ‘group-specific’ PCR primer sets that produce amplicons from a targer group of species, but not from other groups of species. Amplicon assists in group-specific PCR primer desing primarily by being a visualisation tool for alignments from which the user can select regions that may be group-specific primer binding sites. Other useful features that are not common in other PCR primer design software are handling of gapped sequences and degenerate sites in aligned DNA. Group-specific PCR primer sets are useful in a wide variety of situation where environmental DNA is being examined and the diversity or identity of some of the DNA sequences within a sample need to be determined.