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.

[1]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[2]  Elena Bushmanova,et al.  rnaQUAST: a quality assessment tool for de novo transcriptome assemblies , 2016, Bioinform..

[3]  Sarah Machado,et al.  LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation , 2019, BMC Bioinformatics.

[4]  Justin Zobel,et al.  Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.

[5]  Brian Bushnell,et al.  BBMerge – Accurate paired shotgun read merging via overlap , 2017, PloS one.

[6]  P. Pevzner,et al.  Plasmid detection and assembly in genomic and metagenomic data sets , 2019, Genome research.

[7]  Elena Bushmanova,et al.  Extending rnaSPAdes functionality for hybrid transcriptome assembly , 2020, BMC Bioinformatics.

[8]  Alla Lapidus,et al.  ExSPAnder: a universal repeat resolver for DNA fragment assembly , 2014, Bioinform..

[9]  Andrey D. Prjibelski,et al.  Assembling short reads from jumping libraries with large insert sizes , 2015, Bioinform..

[10]  Roger S Lasken,et al.  Single-cell genomic sequencing using Multiple Displacement Amplification. , 2007, Current opinion in microbiology.

[11]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[12]  Steven Salzberg,et al.  GAGE-B: an evaluation of genome assemblers for bacterial organisms , 2013, Bioinform..

[13]  Dmitry Antipov,et al.  Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products , 2013, J. Comput. Biol..

[14]  Dmitry Antipov,et al.  hybridSPAdes: an algorithm for hybrid assembly of short and long reads , 2016, Bioinform..

[15]  Alexey A. Gurevich,et al.  MetaQUAST: evaluation of metagenome assemblies , 2016, Bioinform..

[16]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[17]  Hosein Mohimani,et al.  BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs , 2019, Genome research.

[18]  S. Kelly,et al.  TransRate: reference-free quality assessment of de novo transcriptome assemblies , 2015, bioRxiv.

[19]  Elena Bushmanova,et al.  rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data , 2018, bioRxiv.

[20]  Alla Lapidus,et al.  IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction , 2019, J. Comput. Biol..

[21]  Paul Medvedev,et al.  Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..

[22]  Sergey I. Nikolenko,et al.  BayesHammer: Bayesian clustering for error correction in single-cell sequencing , 2012, BMC Genomics.

[23]  Manja Marz,et al.  De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers , 2019, GigaScience.

[24]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[25]  Dmitry Antipov,et al.  plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data , 2016, bioRxiv.

[26]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[27]  Wei Li,et al.  RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..

[28]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..