The new version introduces a lot of major features for NGS data analysis:
Quality control: a new tool Trimmomatic was integrated for quality control of NGS reads. It allows one to cut Illumina adapters, trim reads ends by quality, trim reads by length, etc.
De novo assembly: SPAdes was updated to version 3.12.0. Graphical interface for the tool in UGENE was updated. It is now possible to input hybrid data, for example, assemble Illumina and Oxford Nanopore reads.
Metagenomics: a new infrastructure for taxonomy classification of whole-genome shotgun sequencing data was developed. This includes tools Kraken, CLARK, DIAMOND, WEVOTE and other. Reference data for the tools are also provided: NCBI taxonomy information; RefSeq data for viruses, bacteria, human; etc.
Transcriptomics: a new tool StringTie was integrated.
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