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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 ...
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. [ 2 ] [ 3 ] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments ...
PeaZip is a free and open-source file manager and file archiver [5] for Microsoft Windows, ReactOS, [6] Linux, [7] [8] [9] MacOS [10] and BSD [11] [12] by Giorgio Tani. It supports its native PEA archive format [ 13 ] (supporting compression, multi-volume split, and flexible authenticated encryption and integrity check schemes) and other ...
The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present.
^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality $ (dollar) marks the end of a read segment * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the - [0-9] + [ACGTNacgtn] + notation
bam-lorenz-coverage A tool that can generate Lorenz plots and Coverage plots, or export these statistics to text files, directly from BAM file(s). [ 7 ] dupRadar [ 8 ] An R package which provides functions for plotting and analyzing the duplication rates dependent on the expression levels.
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7-Zip is a free and open-source file archiver, a utility used to place groups of files within compressed containers known as "archives". It is developed by Igor Pavlov and was first released in 1999. [2] 7-Zip has its own archive format called 7z introduced in 2001 [12], but can read and write several others.