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While standard data compression tools (e.g., zip and rar) are being used to compress sequence data (e.g., GenBank flat file database), this approach has been criticized to be extravagant because genomic sequences often contain repetitive content (e.g., microsatellite sequences) or many sequences exhibit high levels of similarity (e.g., multiple genome sequences from the same species).
SAMtools makes it possible to work directly with a compressed BAM file, without having to uncompress the whole file. Additionally, since the format for a SAM/BAM file is somewhat complex - containing reads, references, alignments, quality information, and user-specified annotations - SAMtools reduces the effort needed to use SAM/BAM files by ...
Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised by Markus Hsi-Yang Fritz et al. [1] CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file ...
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files.
While data reduction (compression, be it lossy or lossless) is a main goal of transform coding, it also allows other goals: one may represent data more accurately for the original amount of space [5] – for example, in principle, if one starts with an analog or high-resolution digital master, an MP3 file of a given size should provide a better ...
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Data compression aims to reduce the size of data files, enhancing storage efficiency and speeding up data transmission. K-means clustering, an unsupervised machine learning algorithm, is employed to partition a dataset into a specified number of clusters, k, each represented by the centroid of its points. This process condenses extensive ...
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