Safe and Complete Contig Assembly Via Omnitigs

  title={Safe and Complete Contig Assembly Via Omnitigs},
  author={Alexandru I. Tomescu and Paul Medvedev},
Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be… Expand
10 Citations
Genome assembly, from practice to theory: safe, complete and linear-time.
  • 1
  • PDF
A safe and complete algorithm for metagenomic assembly
  • 5
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era
  • 3
  • PDF
An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph
  • 4
  • PDF
Safely Filling Gaps with Partial Solutions Common to All Solutions
  • 5
  • PDF
deBWT: parallel construction of Burrows–Wheeler Transform for large collection of genomes with de Bruijn-branch encoding
  • 11
  • Highly Influenced
  • PDF
Safety in s-t Paths, Trails and Walks
  • PDF


Scaffolding pre-assembled contigs using SSPACE
  • 1,876
  • PDF
BESST - Efficient scaffolding of large fragmented assemblies
  • 107
  • PDF
Efficient de novo assembly of large genomes using compressed data structures.
  • 709
  • PDF
Efficient construction of an assembly string graph using the FM-index
  • 240
  • PDF
The fragment assembly string graph
  • E. Myers
  • Mathematics, Medicine
  • 2005
  • 398
  • Highly Influential
  • PDF
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
  • 681
  • PDF
Maximum Likelihood Genome Assembly
  • 114
  • PDF
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers
  • 42
  • PDF
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
  • 8,598
  • PDF
Assembly complexity of prokaryotic genomes using short reads
  • 213
  • Highly Influential
  • PDF