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First, one protein-coding gene atpF have 15,121, 3,030, and 91 corresponding cDNA reads, accounting for 79.4%, 66.8%, and 21.9% of the total cp related reads in leaf, root, and bud, respectively.
In the last consensus step, each position in the target sequence is determined by several related reads.
For a given read r c, there are total (m − k) k-mers and n rc related reads.
Skim3 as part of the MIRA program is an algorithm related to SSAHA [ 43], which is used for a pre-selection of related reads.
To achieve this, we introduce the novel concept of virtual contigs, which are longer than traditional contigs because they are not, strictly speaking, contigs but functionally help to connect related reads together as a single unit for binning purposes, e.g. reads/contigs are binned together by paired-end reads or substantially-overlapped regions.
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