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. 2014 Dec 2;9(12):e114253. doi: 10.1371/journal.pone.0114253

Figure 1. Workflow of PERGA.

Figure 1

There are two phases for PERGA. assembly of reads and assembly of contigs. (A) Phase 1, assembly of reads. k-mer hash table is firstly constructed using paired-end reads for k = O min, then contigs are extended iteratively one base at a time (left feedback loop) at 3′ end by using paired-end reads in high priority, and variable overlap size thresholds ranging from O max to O min (right feedback loop) if there are no paired-ends. (B) Phase 2, scaffolding. Paired-end reads are used to order and orient contigs, fill intra-scaffold gaps to generate larger scaffolds.