Run AmpliSAS

Run name:
Email (optional):
Sequence file: FASTA/FASTQ (compressed or uncompressed) without spaces, parenthesis or other special symbols in the name
If reads have been already de-multiplexed into separate files (one file per sample), you can pack them into a single .zip or .tar.gz format file and use it as input. In such case you should leave empty the amplicon data section.
Max. 500 MB Download example

Or file URL:

Technology: Auto Illumina 454/IonTorrent      Analysis parameters will be optimized for the selected sequencing technology, they can be modified in "Advanced options".

If transcriptomic data is being analyzed or many co-amplifying alleles are expected (>10, e.g. MHC class I), the 'minimum per amplicon frequency' threshold in 'Advanced program parameters' section should be manually adjusted.
Maximum number of alleles per amplicon: Maximum number of expected alleles per amplicon, it will limit the number of clusters to calculate and also this number will be used for Degree of Change calculations in case this filtering option is chosen.
Minimum amplicon depth: Amplicons with lower total coverage will be discarded.
Amplicon data: It is very important to specify all the primer and tag sequences in 5'->3' sense.
Shortening primer sequences to 7-9 nts can increase the number of retrieved sequences (eg. GAGTGTCAT instead of GAGTGTCATTTCTCCAACGGGA).

or file: Max. 100 KB See example

Alleles file (optional): FASTA format Max. 2 MB See example

Additional options:

Only de-multiplexing: If selected this option, sequences/reads will be de-multiplexed into amplicons (very fast, clustering and filtering steps will be skipped).
Skip clustering: If selected this option, clustering step will be skipped and clustering parameters will be ignored.
Skip filtering: If selected this option, filtering step will be skipped and filtering parameters will be ignored.
Verbose mode:
All sequences clustered and/or filtered will be printed into individual files explaining the clustering/filtering reasons.
Maximum number of reads per amplicon: Maximum number of amplicon sequences/reads to be processed.

Advanced program parameters


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