Amptools is a set of tools for describing and analysing amplicon experiments sequenced using massively parallel DNA sequencers. The tools are generally based around the SAM format and layer in some extra information that reflects the needs of an amplicon sequencing experiment.

Amplicon sequencing experiments are based around amplification of specific genomic regions which are then pooled for sequencing. A given experiment may involve multiple amplicons and multiple samples. We want to be able to answer questions such as

• What is the distribution of the number of reads per amplicon?
• Are any observed variants seen on multiple amplicons, or are particular amplicons biased?

Amptools can help with these questions and typical steps involved in processing an amplicon experiment.

A simple strategy for removing primers from sequencing reads looks for reads with the primers and removes the primer sequence. However, in a tiled amplicon experiment, primer sequence for one amplicon may be genomic sequence for another amplicon. Amptools therefore offers a method for primer trimming mapped reads, where the actual amplicon that produced the read can be identified unambiguously.

PCR duplicates are usually detected in sequencing experiments by finding reads with the same start position and orientation. Since all reads from the same amplicon match this criteria another approach must be used. Amptools supports the inclusion of random degenerate bases in the adaptor which can be used to detect PCR duplicates.

Amptools uses two SAM read tags to add information to a SAM file:

• The amplicon name are stored in AM
• Degenerate bases are stored in DB