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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 ...
The browser allows users to visualize and browse large (up to hundreds of millions of short reads) next generation sequence assemblies. It supports SAM, [20] BAM (the binary version of SAM), and ACE formats. Before browsing assembly data in UGENE, an input file is converted to a UGENE database file automatically. This approach has its pros and ...
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.
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
The operating systems the archivers can run on without emulation or compatibility layer. Ubuntu's own GUI Archive manager, for example, can open and create many archive formats (including Rar archives) even to the extent of splitting into parts and encryption and ability to be read by the native program .