A full analysis pipeline can be built using the OBITools3 (demultiplexing, paired-end reads alignment, dereplicating, global alignment, PCR error detection, taxonomic assignment, annotation using taxonomic information if necessary, in silico PCR…).

This new version of the OBITools looks to significantly improve the storage efficiency and the data processing speed by relying on an ad hoc database system.

Languages: C / Python / Cython

https://metabarcoding.org/obitools3

Sumatra computes the exact pairwise global alignment scores from one dataset or between two datasets.

Used: lossless kmer filter / optimized exact alignment / SIMD parallelization / pthreads parallelization
Languages: C

https://metabarcoding.org/sumatra

Sumaclust clusters sequences using the same alignment methods as Sumatra to compute the distance between sequences. The ‘star clustering’ algorithm used is suitable for the quick clustering of a huge number of sequences, and for the detection of ‘erroneous’ sequences created during amplification and sequencing protocols, deriving from ‘true’ sequences.

Used: greedy star-clustering algorithm / lossless kmer filter / optimized exact alignment / SIMD parallelization / OpenMP parallelization
Languages: C

https://metabarcoding.org/sumaclust