AbstractSPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC.Basic Protocol 1: Assembling isolate bacterial datasetsBasic Protocol 2: Assembling metagenomic datasetsBasic Protocol 3: Assembling sets of putative plasmidsBasic Protocol 4: Assembling transcriptomesBasic Protocol 5: Assembling putative biosynthetic gene clustersSupport Protocol 1: Installing SPAdesSupport Protocol 2: Providing input via command lineSupport Protocol 3: Providing input data via YAML formatSupport Protocol 4: Restarting previous runSupport Protocol 5: Determining strand‐specificity of RNA‐seq data