Skip to content

Latest commit

 

History

History
100 lines (66 loc) · 2.33 KB

README_N50_BINNER.md

File metadata and controls

100 lines (66 loc) · 2.33 KB
Raw

n50_binner

This program analyzes a FASTQ file and counts the number of reads falling into predefined length bins.

It can be used to generate a simplified summary of the read length distribution in a FASTQ file, to be then used to generate a similar FASTX file.

What it does

The program:

  1. Reads a (compressed) FASTQ file.
  2. Counts the number of reads falling into each of 16 predefined length bins.
  3. Outputs a CSV-formatted result showing the number of reads in each bin.

How to compile

To compile the program, you need a C compiler (such as gcc) and the zlib library installed. Use the following command:

gcc -o fastq_length_counter fastq_length_counter.c -lz

This will create an executable named fastq_length_counter.

How to use

Run the program from the command line, providing the path to a gzip-compressed FASTQ file as an argument:

./n50_binner path/to/your/file.fastq.gz

The program will process the file and output the results to stdout in CSV format.

Examples

  1. Running the program:
./fastq_length_counter sample.fastq.gz
  1. Saving the output to a file:
./fastq_length_counter sample.fastq.gz > length_distribution.csv
  1. Processing multiple files:
for file in *.fastq.gz; do
    echo "Processing $file"
    ./fastq_length_counter "$file" > "${file%.fastq.gz}_length_distribution.csv"
done

Output format

The output is in CSV format with two columns:

  1. Bin: The upper limit of the length bin
  2. Number of Reads: The count of reads falling into that bin

Example output:

Bin,Number of Reads
10,0
100,5
1000,1000
2500,5000
...

Notes

  • The program uses 16 predefined bins: 10, 100, 1000, 2500, 5000, 10000, 20000, 35000, 50000, 75000, 100000, 200000, 300000, 500000, 750000, and 1000000.
  • Reads longer than 1,000,000 bases will be counted in the last bin.
  • The program assumes the input file is in the standard FASTQ format and is gzip-compressed.

Dependencies

  • zlib library for reading gzip-compressed files

Remember to install zlib development files before compiling. On Ubuntu or Debian, you can do this with:

sudo apt-get install zlib1g-dev

License

This program is provided under the MIT License. See the source code for full license text.

Author

Andrea Telatin, 2023 Quadram Institute Bioscience