De Novo Genome Assembly

De novo sequencing refers to sequencing a novel genome where there is no reference sequence available for alignment. Sequence reads are assembled as contigs, and the coverage quality of de novo sequence data depends on the size and continuity of the contigs (ie, the number of gaps in the data).

Parameters

$n$ : sum of lengths of reads
$f$ : number of input sequences

Filters

Computational Model

Randomization

Approximation

Algorithms Table

Displaying 5 of 5 algorithms


String Graph with Ferragina–Manzini Index (Simpson, Durbin)	2010	$O(n)$	$O(n)$
de Bruijn Graph (Idury, Waterman)	1994	$O(n^2)$	$O(n)$
String Graph (Myers)	1994	$O(n \log n)$	$O(n)$
Overlap Layout Consensus	1987	$O(n^2)$	$O(n^2)$
Greedy SEQAID	1984	$O(n^2)$	$O(n^2)$

Reductions Table

Insuffient Data to display table

Other relevant algorithms

Displaying 1 of 1 other relevant algorithms