CRAM File – What is .cram file and how to open it?
CRAM File Extension
Compressed Alignment File – file format by EBI
CRAM is a binary format for storing large compressed genomic alignments, which preserves all information present in the original SAM/BAM alignment. CRAM employs novel, alignment-specific compression techniques that reduce the file size by a factor of 5-10 compared to BAM, without compromising query performance.
What is a CRAM File?
A CRAM file is a compressed binary format for storing aligned sequencing reads. It was developed by the European Bioinformatics Institute (EBI) to address the need for a more efficient and compact way to store and transmit large volumes of sequencing data. CRAM files are based on the SAM/BAM format, which is the standard format for representing aligned sequencing reads. However, CRAM files use a more efficient compression algorithm that can reduce the file size by up to 10-fold compared to BAM files.
Advantages of CRAM Files
CRAM files offer several advantages over BAM files, including:
- Smaller file size: CRAM files can reduce the file size by up to 10-fold compared to BAM files, making them more efficient to store and transmit.
- Faster loading: CRAM files can be loaded into memory more quickly than BAM files, which can improve the performance of downstream analysis tools.
- Improved compression: CRAM files use a more efficient compression algorithm that can improve the compression ratio compared to BAM files.
- Better support for reference sequences: CRAM files can include a reference sequence, which can be used to align reads and identify variants.
- Support for additional data types: CRAM files can store additional data types, such as quality scores and tags, which can be used for downstream analysis.
Opening CRAM Files with Software
Opening CRAM files requires specialized software programs that are capable of decompressing and interpreting the compressed alignment data. One common tool for this purpose is SAMtools, a widely-used suite of utilities for processing and analyzing high-throughput sequencing data. SAMtools includes a command called “samtools view”, which can be used to decompress and convert CRAM files into a more accessible format, such as BAM or FASTA. Another popular software option for opening CRAM files is IGV (Integrative Genomics Viewer), a graphical application for visualizing and exploring genomic data. IGV provides a user-friendly interface for loading and displaying CRAM files, allowing researchers to navigate and analyze the aligned reads.
Additional Considerations
In addition to the software requirements, opening CRAM files may also require additional considerations. CRAM files often contain large amounts of data, so it is important to ensure that your computer has sufficient memory and storage space to handle the processing. Additionally, certain software programs may require specific versions of CRAM tools or libraries to be installed in order to properly open the files. It is recommended to check the documentation of the software you are using for any specific requirements or dependencies.
CRAM File Structure and Features
CRAM, an abbreviation for Compressed Alignment File, is a file format developed by the European Bioinformatics Institute (EBI) to store compressed genomic alignment data efficiently. It utilizes a combination of lossless compression techniques, including Huffman coding and run-length encoding, to reduce file size while preserving alignment information. Unlike other alignment file formats like BAM/SAM, CRAM stores data in a column-oriented arrangement, allowing for faster data access and reduced memory consumption. Additionally, CRAM supports various data structures, including reads, alignments, and variants, enabling users to store heterogeneous data types in a single file.
Benefits and Applications of CRAM
The compact nature of CRAM files offers significant benefits for efficient storage and analysis of large-scale genomic data. Compared to uncompressed alignment files, CRAM files can achieve compression ratios of up to 90%, reducing storage requirements and facilitating sharing and transfer of data. The column-oriented storage structure enables rapid retrieval of specific data segments, such as reads or alignments, without the need to decompress the entire file. Furthermore, CRAM supports the progressive loading of data, allowing users to dynamically load data subsets on demand, thereby optimizing memory usage and improving performance. Its versatility in storing multiple data types makes CRAM a suitable choice for integrating different types of genomic information for comprehensive analysis.