AmpliSAS - Amplicon Sequencing ASsignment tool
accomplishes a full analysis of the data: de-multiplexation, clustering and filtering of variants (unique sequences) with genotyping purposes.
After running AmpliCHECK we should be able to establish the length of the desired PCR products (markers), the % of errors in variants and a threshold frequency to decide if a variant is real or is an artefact. Then we can run AmpliSAS to perform an exhaustive analysis and genotyping.
AmpliSAS workflow is divided into three main steps:
- De-multiplexing of reads into amplicons and unique sequences based on matching of primers and tags sequences.
- Clustering of amplicon sequences, where potential alleles and artefacts are grouped together based on user-defined thresholds.
- Filtering of sequences based on user-defined parameters, like number of samples, frequency, depth, chimeras and frameshifts detection...
AmpliSAS takes as input:
- SEQUENCE FILE: FASTQ or FASTA format file (compressed or uncompressed). Multiple sample/amplicon sequence files should be packed into a unique .ZIP or .TAR.GZ file. Also previously analyzed results can be used as input in AmpliSAS format Excel file.
- AMPLICON DATA 1: primer and tag information in a CSV format file as explained in the documentation.
Results can be downloaded on the same page or from an email message after analysis completion.
For more information, read the documentation.