N50 {CNEr} | R Documentation

## Assembly statistics.

### Description

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

### Usage

    N50(fn)
    N90(fn)

### Arguments

`fn` | `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(s)

Ge Tan

### Examples

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

[Package CNEr version 1.18.1 Index]