AssemblyStats: Assembly statistics.
In CNEr: CNE Detection and Visualization

Description Usage Arguments Details Value Author(s) Examples

Calculate the N50, N90 values for a fasta or 2bit file.

1 2	N50(fn) N90(fn)

`fn`	`character`(1): The path of a fasta or 2bit file.

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.

An integer value of N50 or N90 value.

Ge Tan

  twoBitFn <- file.path(system.file("extdata",
                                    package="BSgenome.Drerio.UCSC.danRer10"),
                        "single_sequences.2bit")
  N50(twoBitFn)