To improve the performance, we designed a companion format Binary Alignment/Map (BAM), which is the binary representation of SAM and keeps exactly the same information as SAM. BAM is compressed by the BGZF library, a generic library developed by us to achieve fast random access in a zlib-compatible compressed file. An example alignment of 112 Gbp of Illumina GA data requires 116 GB of disk space (1.0 byte per input base), including sequences, base qualities and all the meta information generated by MAQ. Most of this space is used to store the base qualities.
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Optimizing Genome Sequence Storage
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Companion
Generic
Library
Corresponding Organization :
Other organizations : Beijing Institute of Genomics, University of California, Los Angeles, Broad Institute, Wellcome Sanger Institute, Boston College
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Variable analysis
independent variables
- Designed a companion format Binary Alignment/Map (BAM), which is the binary representation of SAM and keeps exactly the same information as SAM
- BAM is compressed by the BGZF library, a generic library developed by us to achieve fast random access in a zlib-compatible compressed file
- Performance
- Disk space required for an example alignment of 112 Gbp of Illumina GA data (116 GB, including sequences, base qualities and all the meta information generated by MAQ)
- Maintained the same information as SAM in the BAM format
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