README_N50.md

n50 - Calculate N50

A fast and efficient tool for calculating N50 and other sequence statistics from FASTA and FASTQ files.

Features

• Supports both FASTA and FASTQ formats
• Optimized for FASTQ raw file (Nanopore, PacBio)
• Handles gzipped input files

Installation

Prerequisites

• GCC compiler
• zlib library
• pthread library

Compiling

To compile the program, use the following command:

make

or compile binaries like:

gcc -o n50 src/n50.c -lz -lpthread -O3

Usage

./n50 [options] [filename]...

If no filename is provided, the program reads from standard input.

Options

• --fasta or -a: Force FASTA input format
• --fastq or -q: Force FASTQ input format
• --header or -H: Print header in the output
• --n50 or -n: Output only the N50 value
• --version and --help to display version and help information respectively

Examples

1. Process a FASTA file:

./n50 input.fasta

2. Process a gzipped FASTQ file:

./n50 input.fastq.gz

3. Process a file with header output:

./n50 --header input.fasta

4. Output only the N50 value:

./n50 --n50 input.fasta

5. Process input from stdin:

cat input.fasta | ./n50 --format fasta

Output

By default, the program outputs a tab-separated line with the following fields:

1. Format (FASTA or FASTQ)
2. Total sequence length
3. Total number of sequences
4. N50 value

When using the --header option, a header line is printed before the results.

When using the --n50 option, only the N50 value is printed.

Performance

The program uses multi-threading to process large files efficiently. It automatically adjusts the number of threads based on the input size, up to a maximum of 8 threads.

Limitations

• The maximum number of threads is currently set to 8. This can be adjusted by modifying the MAX_THREADS constant in the source code.
• The initial capacity for storing sequence lengths is set to 1,000,000. For extremely large datasets, this value might need to be increased.