Using SPAdes De Novo Assembler

SPAdes—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 datasets

Basic Protocol 2: Assembling metagenomic datasets

Basic Protocol 3: Assembling sets of putative plasmids

Basic Protocol 4: Assembling transcriptomes

Basic Protocol 5: Assembling putative biosynthetic gene clusters

Support Protocol 1: Installing SPAdes

Support Protocol 2: Providing input via command line

Support Protocol 3: Providing input data via YAML format

Support Protocol 4: Restarting previous run

Support Protocol 5: Determining strand-specificity of RNA-seq data