SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

SEED2 is a free to use graphical user interface-based sequence editor and NGS data analysis pipeline for all Windows platforms with 64-bit architecture designed to guide users intuitively through the data analysis workflow. SEED2 was created to provide an intuitive interface for fast bioinformatic analysis of PCR amplicons from NGS (such as the bacterial 16S or fungal ITS amplicons) according to the suggested workflow. SEED2 is fully optimized for Illumina data and has the capacity to process whole Illumina MiSeq run on a standard personal computer with 16 GB RAM. The pipeline has a wide array of functions including the editing of sequences and their titles, sorting, quality trimming, pair-end joining, grouping of sequences based on sequence motifs or titles, batch processing of sequence groups, chimera removal, ITS extraction, sequence alignments and clustering, OTU table construction, construction of consensus sequences, creation of local databases for BLAST and searching within them or in the whole NCBI, retrieval of taxonomical classification from the NCBI, calculation of diversity parameters. Newly, it also covers tools to construct and edit phylogenetic trees. We believe that the pipeline is not only useful for processing of high-throughput amplicon data, but also for fast and easy editing and formatting of any large sequence datasets under the Windows environment. The latest version of SEED2 is Seed2.1_64bit.


Vetrovsky, T., Baldrian, P. and Morais, D. (2018) "SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses." Bioinformatics, bty071, 2018 (https://doi.org/10.1093/bioinformatics/bty071)