Evaluation for <i>E.coli</i> simulated short reads data (D1, 50×).

<p>Evaluation for <i>E.coli</i> simulated short reads data (D1, 50×).</p

Evaluation for human chromosome 14 real short reads data (D8, 40×).

<p>Evaluation for human chromosome 14 real short reads data (D8, 40×).</p

Scheme for removing erroneous bases.

<p>Erroneous bases in reads will cause dead ends and bubbles that can be implicitly resolved as these errors can be masked by these correct reads. Reads with low similarities probably can be assembled onto other contigs with higher similarity.</p

Evaluation for <i>E.coli</i> real short reads data (D4, 600×).

<p>Evaluation for <i>E.coli</i> real short reads data (D4, 600×).</p

Evaluation for human chromosome 14 simulated short reads data (D7, 50×).

<p>Evaluation for human chromosome 14 simulated short reads data (D7, 50×).</p

Evaluation for <i>S.pombe</i> real short reads data (D6, 52×).

<p>Evaluation for <i>S.pombe</i> real short reads data (D6, 52×).</p

Statistical results for look-ahead approach.

<p>Statistical results for look-ahead approach.</p

Workflow of PERGA.

<p>There are two phases for PERGA. assembly of reads and assembly of contigs<b>.</b> (A) Phase 1, assembly of reads. <i>k</i>-mer hash table is firstly constructed using paired-end reads for <i>k</i> = <i>O</i>_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 <i>O</i>_max to <i>O</i>_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.</p