Gap Filling as Exact Path Length Problem

@inproceedings{Salmela2015GapFA,
  title={Gap Filling as Exact Path Length Problem},
  author={Leena Salmela and Kristoffer Sahlin and Veli M{\"a}kinen and Alexandru I. Tomescu},
  booktitle={RECOMB},
  year={2015}
}
One of the last steps in a genome assembly project is filling the gaps between consecutive contigs in the scaffolds. This problem can be naturally stated as finding an \(s\)-\(t\) path in a directed graph whose sum of arc costs belongs to a given range (the estimate on the gap length). Here \(s\) and \(t\) are any two contigs flanking a gap. This problem is known to be NP-hard in general. Here we derive a simpler dynamic programming solution than already known, pseudo-polynomial in the maximum… CONTINUE READING
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Safely Filling Gaps with Partial Solutions Common to All Solutions

  • IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2019
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References

Publications referenced by this paper.
SHOWING 1-10 OF 22 REFERENCES

Toward almost closed genomes with GapFiller

  • Genome Biology
  • 2012
VIEW 11 EXCERPTS
HIGHLY INFLUENTIAL

ABySS: a parallel assembler for short read sequence data.

  • Genome research
  • 2009
VIEW 6 EXCERPTS
HIGHLY INFLUENTIAL

The Exact Path Length Problem

  • J. Algorithms
  • 2002
VIEW 9 EXCERPTS
HIGHLY INFLUENTIAL