spadesSPAdes (St. Petersburg genome assembler) is a versatile toolkit for genome assembly of isolate, single-cell, metagenomic, transcriptomic, plasmid, and viral sequencing data. It supports Illumina, IonTorrent, PacBio, and Nanopore reads, and includes specialized runs for plasmid, metagenome, viral, and RNA-Seq pipelines.Versions

v4.3.0 (default)

Tags: genome assembly, bioinformatics, de novo, bacterial, metagenomics, transcriptomics, plasmids, viralParameters

type (enum) required. Options: paired-end, interlaced, single, pacbio, nanopore

pe1 (file): Forward paired-end reads.

pe2 (file): Reverse paired-end reads.

twelve (file): Interlaced forward+reverse paired-end reads.

single (file): Unpaired reads.

pacbio (file): PacBio reads.

nanopore (file): Nanopore reads.

mode (enum) required: Pipeline mode (isolate, meta, plasmid, etc.). Options: isolate, sc, meta, bio, sewage, corona, rna, plasmid and 5 more

Links

License: GPL-2.0-only

Cite as: Bankevich, A., et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol., 19(5): 455-477 (2012). https://doi.org/10.1089/cmb.2012.0021 For protocol: Prjibelski, A.D., et al. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020; 70(1):e102. https://doi.org/10.1002/cpbi.102 For metaSPAdes, plasmidSPAdes, see additional publications at https://ablab.github.io/spades/citation.html.

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