Using SPAdes De Novo Assembler

By Andrey D. Prjibelski, Dmitry Antipov, Dmitry Meleshko, Alla L. Lapidus, Anton I. Korobeynikov. Current Protocols in Bioinformatics, 2020

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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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/673b94c24e88398dce26f75a101976f85030f87a

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Citations in the corpus

Sequence Analysis (2020, positive): “Although Loop-Seq pipeline involves the assembly of individual read clouds (reads sharing identical barcode sequence) using the SPAdes assembler (Prjibelski et al. 2020), it can only be applied when the coverage within a cloud is sufficient, which is often not the case, particularly for the…”
Pangenomics enables genotyping known structural variants in 5,202 diverse genomes (2021, methodology): “The graphical fragment assembly (GFA) format for representing pangenome graphs has increasing tool support, including by vg ( 12 , 39 – 43 ).”