Here is a list of software developed by our laboratory.

AmpliSAT - Amplicon Sequence Analysis Tools: set of online tools for data analysis of Amplicon Sequencing experiments. Currently it includes: AmpliSAS, AmpliCHECK, AmpliCOMPARE, AmpliLEGACY, AmpliMERGE, AmpliCLEAN and AmpliCOMBINE.

AmpliSAS - Amplicon Sequencing ASsignment tool

accomplishes a full analysis of the data: de-multiplexation, clustering and filtering of unique sequences.

After de-multiplexation, sequences are pairwise aligned and erroneus sequences (artifacts) are identified and grouped with real ones using as clustering criteria technique specific error-rates. At the end, non clustered and low frequency sequences are filtered and removed to obtain an Excel file with unique sequence assignations for each amplicon analyzed. Choosing the rigth parameters we will be able to perform reliable genotypings with AmpliSAS.

Before using AmpliSAS is highly recommended to run AmpliCHECK to have a glance at the most common sequences and their putative sequencing errors (artifacts). AmpliCHECK annotates the differences between unique sequences and gives a preliminar idea of the analysis complexity. After that, AmpliSAS will group artifacts with real sequences, increasing their coverages and giving a simplified output that can be used as a guide in the genotyping task.

AmpliSAS working schema:

AmpliCHECK - Amplicon Sequencing CHECKing tool

AmpliCHECK is intended for a preliminary analysis of amplicon sequencing results.

It performs de-multiplexation of reads and checks, amplicon by amplicon, major unique sequences to annotate their similarities. This annotation will help in the identification of real alleles and artifacts. Results are retrieved in an Excel file, coloring in green, yellow and red, putative real sequences, questionable ones and clear artifacts respectively.

AmpliCHECK working schema:

Subpages (3): AmpliCHECK AmpliSAS AmpliSAT