Base calling

Base Calling is a critical process in bioinformatics and genomics, where it is used to determine the sequence of nucleotides in a DNA or RNA molecule. The process involves the interpretation of raw data produced by sequencing technologies to identify the specific nucleotides (adenine, guanine, cytosine, and thymine in DNA; adenine, guanine, cytosine, and uracil in RNA).

Process

The base calling process begins with the collection of raw data from a sequencing machine. This data is typically in the form of fluorescent signals or electrical signals, which correspond to the different nucleotides. The signals are then processed using a base calling algorithm, which interprets the signals and assigns a nucleotide base to each one. The result is a sequence of bases, which represents the sequence of nucleotides in the DNA or RNA molecule.

Base Calling Algorithms

There are several different algorithms used for base calling, each with its own strengths and weaknesses. Some of the most commonly used algorithms include:

• Phred base calling algorithm: This is one of the most widely used base calling algorithms. It is known for its accuracy and reliability, and it provides a quality score for each base call, which indicates the confidence of the call.

• Illumina base calling algorithm: This algorithm is used in Illumina sequencing machines. It uses a probabilistic model to interpret the raw data and make base calls.

• ABI base calling algorithm: This algorithm is used in Applied Biosystems sequencing machines. It uses a combination of signal processing and pattern recognition techniques to make base calls.

Challenges

Despite the advances in base calling algorithms, there are still several challenges associated with base calling. These include:

• Signal degradation: Over time, the quality of the signals produced by the sequencing machine can degrade, making it more difficult to accurately call bases.

• Sequencing errors: Errors can occur during the sequencing process, leading to incorrect base calls.

• Homopolymer sequences: These are sequences of the same nucleotide repeated multiple times. They can be difficult to accurately call due to signal overlap.

See Also

• DNA sequencing
• Next-generation sequencing
• Bioinformatics