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De Novo Genome Assembly

The Greedy Shortest Common Superstring

Task

  • In R, implement a function GreedySuperstring() according to the pseudocode.

  • Input:

    • S A DNAStringSet of strings (reads).

  • Output:

    • S A DNAStringSet of the shortest common superstring (contig).

Hint: Create also functions:

  • Overlap() to calculate overlap between two sequences.
  • OverlapMatrix() to create a matrix of overlaps among all sequences in S.
GreedySuperstring(S)
1   while length of S > 1
2     overlapMat <- OverlapMatrix(S)
3     if max(overlapMat) = 0
4       return S
5     else
6       seq1, seq2 ← Two sequences from S with the longest overlap
7       Merge seq1 and seq2 and add the new sequence to S
8       Remove seq1 and seq2 from S
9   return S
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Basic Git settings
  • Configure the Git editor 
    git config --global core.editor notepad
  • Configure your name and email address 
    git config --global user.name "Zuzana Nova"
git config --global user.email [email protected]
  • Check current settings 
    git config --global --list

  • Create a fork on your GitHub account. On the GitHub page of this repository find a Fork button in the upper right corner.

  • Clone forked repository from your GitHub page to your computer:

git clone <fork repository address>
  • In a local repository, set new remote for a project repository:
git remote add upstream https://github.com/mpa-prg/exercise_09.git

Send files to GitHub

Create a new commit and send new changes to your remote repository.

  • Add file to a new commit.
git add <file_name>
  • Create a new commit, enter commit message, save the file and close it.
git commit
  • Send a new commit to your GitHub repository.
git push origin main