Class 12

May 10th, 2016

Welcome to the last class

of “Computing for Molecular Biology 2”

Plan for Today

Experimental Design
Simulation

Genome Assembly

Genome Assembly

Genome Assembly

Genome Assembly

Genome Assembly

Gap counter

num.gaps <- function(G,L,n) {
  start <- sample(G, n, replace=TRUE)
  start <- sort(start)
  end <- start + L
  return(sum(start[-1] > end[-length(end)]))
}

G: Length of genome
L: Length of fragment/read
n: number of fragments/reads

Gap counter

num.gaps <- function(G,L,n) {
  start <- sample(G, n, replace=TRUE)
  start <- sort(start)
  end <- start + L
  gap <- start[-1] - end[-length(end)]
  return(sum(gap > 0))
}

Gap counter

num.gaps <- function(G,L,n) {
  start <- sample(G, n, replace=TRUE)
  start <- sort(start)
  end <- start + L
  overlap <- end[-length(end)] - start[-1]
  return(sum(overlap < 0))
}

Contig counter

num.gaps <- function(G,L,n,t) {
  start <- sample(G, n, replace=TRUE)
  start <- sort(start)
  end <- start + L
  overlap <- end[-length(end)] - start[-1]
  return(sum(overlap < t))
}

G: Length of genome
L: Length of fragment/read
n: number of fragments/reads
t: minimum overlap length