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\name{N50}
\alias{N50}
\alias{N90}
\title{
Assembly statistics.
}
\description{
Calculate the N50, N90 values for a fasta or 2bit file.
}
\usage{
N50(fn)
N90(fn)
}
\arguments{
\item{fn}{
\code{character}(1): The path of a fasta or 2bit file.
}
}
\details{
This function calculates the N50, N90 values for an assembly.
The N50 value is calculated by first ordering every contig/scaffold by length
from longest to shortest.
Next, starting from the longest contig/scaffold, the lengths of each contig
are summed, until this running sum equals one-half of the total length of
all contigs/scaffolds in the assembly.
Then the length of shortest contig/scaffold in this list is the N50 value.
Similar procedure is used for N90 but including 90\% of the assembly.
}
\value{
An integer value of N50 or N90 value.
}
\author{
Ge Tan
}
\examples{
twoBitFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
N50(twoBitFn)
}
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