Sequencing

11th Annual Sequencing, Finishing, and Analysis in the Future Meeting
RECENT ADDITIONS TO SPADES FAMILY OF TOOLS
FOR GENOME ASSEMBLY AND ANALYSIS
Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.21)
Alla Lapidus,. Dmitry Antipov, Anton Bankevich, Elena Bushmanova, Alexey Gurevich,
Anton Korobeynikov, Alla Mikheenko, Dmitry Meleshko, Sergey Nurk,
Andrey Prjibelski, Yana Safonova, Pavel Pevzner
Saint Petersburg State University
Despite its central role in genomics, accurate de novo genome assembly remains challenging. Moreover,
the proliferation of new sequencing and sample‐preparation technologies introduces additional
levels of complications. In 2015, the SPAdes genome assembler (Bankevich et al., 2012), that was
originally conceived as a scalable and easy‐to‐modify platform, was gradually extended into a family
of SPAdes tools aimed at various sequencing technologies and applications. In addition to the
constantly updated SPAdes assembler itself, it now includes:
metaSPAdes assembler for metagenomics data (Nurk et al., 2015)
rnaSPAdes: de novo RNA‐seq data assembler (Prjibelsky et al., submitted)
plasmidSPAdes: assembly of plasmids from the whole genome sequencing data (Antipov et al.,
submitted)
dipSPAdes tool for assembly of highly polymorphic genomes (Safonova et al., 2015)
exSPAnder module for repeat resolution that enables efficient utilization of mate‐pair libraries
and even mate‐pairs only assemblies with NexteraMP libraries (Prjibelsky et al., 2014,
Vasilinetc et al., 2015)
hybridSPAdes tool for hybrid assembly of accurate short reads with long error‐prone reads,
such as Pacific Biosciences and Oxford Nanopore reads (Antipov et al., 2015)
truSPAdes tool for assembling Illumina’s barcoded True Synthetic Long Reads (Bankevich and
Pevzner, 2015)
We will provide an overview of the SPAdes family of tools and benchmark them against state‐of‐theart
assembly tools using the QUAST family of assembly evaluation tools:
• QUAST tool for the quality assessment of genomics assemblers (Gurevich et al., 2013)
• metaQUAST tool for the quality assessment of metagenomics assemblers (Mikheenko et al.,
2015)
• rnaQUAST tool for the quality assessment of RNA‐Seq metagenomics assemblers (Bushmanova
et al., 2015)
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