Using SPAdes De Novo Assembler

TLDR

SPAdes was originally developed for de novo assembly of microbial isolates and single‑cell genomic DNA, and later extended to IonTorrent and hybrid short‑ and long‑read assemblies. The article presents five SPAdes assembly pipelines for metagenomes, transcriptomes, plasmids, and biosynthetic gene clusters, along with guidelines and support protocols for proper use. The authors provide five basic assembly protocols (for isolate bacterial, metagenomic, plasmid, transcriptome, and biosynthetic gene cluster datasets) and five support protocols (installation, input specification, YAML format, run restarting, and RNA‑seq strand specificity).

Abstract

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.