NAME

Proch::N50 - Calculate N50 and related statistics for FASTA/FASTQ files with minimal dependencies

VERSION

version 1.7.0

SYNOPSIS

            

              
              
use Proch::N50 qw(getStats getN50);
# Get basic N50
my $n50 = getN50('assembly.fasta');
# Get comprehensive statistics
my $stats = getStats('assembly.fasta');
# Get statistics with JSON output
my $stats_json = getStats('assembly.fasta', 'JSON');
# Get only JSON output
my $json = jsonStats('assembly.fasta');
            
          

DESCRIPTION

A lightweight module to calculate assembly statistics from FASTA/FASTQ files. Provides N50, N75, N90, auN metrics, and sequence length distributions.

getStats()

Calculate N50, N75, N90, auN, and other statistics for a FASTA/FASTQ file.

Parameters: $file - Path to FASTA/FASTQ file $wantJSON - Optional flag to return JSON output $customN - Optional custom N-metric to calculate

Example: my $stats = getStats('assembly.fasta', 'JSON', 80); print $stats->{json};

_calculateMetrics

Internal function to calculate N50, N75, N90, and other metrics

Parameters: \%sizes - Hash reference of sequence lengths and their frequencies $total_size - Total size of all sequences $custom_n - Optional custom N-metric to calculate

Returns: ($n50, $min, $max, $auN, $n75, $n90, $nx)

getN50

Quick function to get only the N50 value for a file.

Parameters: $file - Path to FASTA/FASTQ file

Returns: N50 value or 0 on error

jsonStats

Get statistics in JSON format.

Parameters: $file - Path to FASTA/FASTQ file

Returns: JSON string with statistics or undef on error

BUGS

Please report any bugs or feature requests at: https://github.com/telatin/proch-n50/issues

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2018-2027 by Quadram Institute Bioscience.

This is free software, licensed under:

            

              
              
The MIT (X11) License
            
          

cpanm Proch::N50

perl -MCPAN -e shell
install Proch::N50