IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

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Disease-specific Alterations in the Enteric Virome in Inflammatory Bowel Disease (2015, methodology): “De Novo Contig Assembly Contigs were assembled using the IDBA_UD assembler (v 1.1.0) using minimum and maximum kmer lengths of 20 and 120, respectively (Peng et al., 2012).”
ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples (2019, methodology): “then assembled using the IDBA-UD[34], Trinity[35], SOAPdenovo, and SOAPdenovo-Trans[36] assemblers.”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, background): “A growing number of assemblers (Boisvert et al., 2012; Peng et al., 2012) and binning tools (Alneberg et al., 2014; Imelfort et al., 2014; Nurk et al., 2017) are available that assemble short sequencing reads into larger contigs and subsequently combine them into bins based on, for example,…”
SKESA: strategic k-mer extension for scrupulous assemblies (2018, background): “Some are specialized for ploidity [29], metagenomes [30–35], single cell [36], sequencing technologies [37], or combine several assemblies into one [38].”