SPAdes Family of Tools for Genome Assembly and Analysis: What's New?

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... [ view full abstract ]

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. 

Recently 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., 2017)
• rnaSPAdes: de novo RNA‐seq data assembler (Prjibelsky et al., submitted)
• plasmidSPAdes: assembly of plasmids from the whole genome sequencing data (Antipov et al., 2016)
• 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 module for hybrid assembly of accurate short reads with long error‐prone reads, such as Pacific Biosciences and Oxford Nanopore reads (Antipov et al., 2015)
• antiSPAdes tool aimed to accurate reconstruction of biosynthetic gene clusters using their domain structure (Meleshko et al., in preparation)