De Novo Genome Assembly: Difference between revisions
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== Parameters == | == Parameters == | ||
$n$: sum of lengths of reads | |||
$f$: number of input sequences | |||
== Table of Algorithms == | == Table of Algorithms == | ||
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| [[de Bruijn Graph (Idury, Waterman) (De Novo Genome Assembly De Novo Genome Assembly)|de Bruijn Graph (Idury, Waterman)]] || 1994 || $O(n^{2})$ || $O(n)$? || Exact || Deterministic || [https://www-ncbi-nlm-nih-gov.ezproxy.canberra.edu.au/pubmed/7497130 Time] | | [[de Bruijn Graph (Idury, Waterman) (De Novo Genome Assembly De Novo Genome Assembly)|de Bruijn Graph (Idury, Waterman)]] || 1994 || $O(n^{2})$ || $O(n)$? || Exact || Deterministic || [https://www-ncbi-nlm-nih-gov.ezproxy.canberra.edu.au/pubmed/7497130 Time] | ||
|- | |- | ||
| [[String Graph (Myers) (De Novo Genome Assembly De Novo Genome Assembly)|String Graph (Myers)]] || 1994 || $O( | | [[String Graph (Myers) (De Novo Genome Assembly De Novo Genome Assembly)|String Graph (Myers)]] || 1994 || $O(n \log n)$ || $O(n)$? || Exact || Deterministic || [https://www-ncbi-nlm-nih-gov.ezproxy.canberra.edu.au/pubmed/7497129 Time] | ||
|- | |- | ||
| [[String Graph with Ferragina–Manzini Index (Simpson, Durbin) (De Novo Genome Assembly De Novo Genome Assembly)|String Graph with Ferragina–Manzini Index (Simpson, Durbin)]] || 2010 || $O(n)$ || $O(n)$? || Exact || Deterministic || [https://www-ncbi-nlm-nih-gov.ezproxy.canberra.edu.au/pmc/articles/PMC2881401/pdf/btq217.pdf Time] | | [[String Graph with Ferragina–Manzini Index (Simpson, Durbin) (De Novo Genome Assembly De Novo Genome Assembly)|String Graph with Ferragina–Manzini Index (Simpson, Durbin)]] || 2010 || $O(n)$ || $O(n)$? || Exact || Deterministic || [https://www-ncbi-nlm-nih-gov.ezproxy.canberra.edu.au/pmc/articles/PMC2881401/pdf/btq217.pdf Time] | ||
Revision as of 08:22, 10 April 2023
Description
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
Table of Algorithms
| Name | Year | Time | Space | Approximation Factor | Model | Reference |
|---|---|---|---|---|---|---|
| Overlap Layout Consensus | 1987 | $O(n^{2})$ | $O(n^{2})$? | Deterministic | ||
| Greedy SEQAID | 1984 | $O(n^{2})$? | $O(n^{2})$? | Deterministic | Time | |
| de Bruijn Graph (Idury, Waterman) | 1994 | $O(n^{2})$ | $O(n)$? | Exact | Deterministic | Time |
| String Graph (Myers) | 1994 | $O(n \log n)$ | $O(n)$? | Exact | Deterministic | Time |
| String Graph with Ferragina–Manzini Index (Simpson, Durbin) | 2010 | $O(n)$ | $O(n)$? | Exact | Deterministic | Time |
| Hybrid Algorithm | 1999 | $O(n^{2})$ | Exact | Deterministic |
Time Complexity Graph
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Space Complexity Graph
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Time-Space Tradeoff
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