What File Type Are Made for NGS Data?


Larry Thompson

What File Types Are Made for NGS Data?

Next-generation sequencing (NGS) has revolutionized the field of genomics by enabling high-throughput sequencing of DNA and RNA molecules. With the generation of massive amounts of data, it is essential to understand the different file types that are commonly used to store NGS data. In this article, we will explore the most prevalent file formats for NGS data and their characteristics.


One of the most widely used file formats for NGS data is the FASTQ format. FASTQ files contain both sequence and quality score information. Each sequence read is represented by four lines:

  1. @SequenceID: A unique identifier for the sequence read.
  2. Sequence: The actual nucleotide sequence.
  3. “+ “: A separator line.
  4. Quality Scores: Encoded representation of the quality scores corresponding to each base in the sequence.

BAM Files

BAM (Binary Alignment/Map) files are binary representations of DNA or RNA sequence alignments against a reference genome. These files are compressed and indexed, allowing for efficient storage and retrieval of alignment information. BAM files also store additional metadata such as read group information, mapping qualities, and alignment flags.

VCF Files

VCF (Variant Call Format) files are used to store genomic variations detected from NGS data. These variations can include single nucleotide polymorphisms (SNPs), insertions, deletions, and structural variants. VCF files consist of structured columns containing information about each variant, including its genomic position, reference allele, alternate allele(s), and quality scores.


FASTA files contain nucleotide or protein sequences, without quality score information. Each sequence is represented by a header line starting with the “>” symbol, followed by one or more lines containing the actual sequence.

CRAM Files

CRAM (Compressed RAM) files are similar to BAM files but provide further compression for NGS data. CRAM files use reference-based compression, where only the differences between the aligned reads and the reference genome are stored. This allows for significant reduction in file size while retaining the necessary information for downstream analysis.


In this article, we have explored some of the most commonly used file formats for NGS data. The FASTQ format is used to store raw sequencing reads along with their quality scores.

BAM files are binary representations of aligned sequences against a reference genome, while VCF files store genomic variations. FASTA files contain sequences without quality scores, and CRAM files offer compressed storage of NGS data.

Understanding these file formats is crucial for working with NGS data efficiently and accurately. Each format serves a specific purpose in genomics research and analysis. By familiarizing ourselves with these file types, we can make better use of the vast amount of information generated by next-generation sequencing.

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