A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

Algorithm 1

The algorithm for scaffold construction. ConPath uses a simple greedy algorithm to obtain a feasible heuristic solution for an NP-complete problem.

 MakeScaffold(mate-pair set)

 {

  initial scaffold graph 𝐆=(𝐕,𝐄;𝐕={allcontigs},𝐄={})

  assign each mate-pair to corresponding an edge → edge set 𝐄

  remove self-collision mate-pairs

  while (edge set 𝐄 is not empty)

   find an edge with maximum weight from 𝐄→𝐞(𝐤,1)

   if (𝐞(𝐤,1) does not conflict with 𝐆)

    add 𝐞(𝐤,1) to graph 𝐆

   delete 𝐞(𝐤,1) from edge set 𝐄

 end while

 }