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As sorting is memory intensive and BAM files can be large, this command supports a sectioning mode (with the -m options) to use at most a given amount of memory and generate multiple output file. These files can then be merged to produce a complete sorted BAM file [TODO - investigate the details of this more carefully].
Changes made to the command line environment after SetLocal commands are local to the batch file. EndLocal command restores the previous settings. [17] The Call command allows subroutines within batch file. The Call command in COMMAND.COM only supports calling external batch files. File name parser extensions to the Set command are comparable ...
Since the RD (RMDIR) command can not delete a directory if the directory is not empty (except in Windows NT & 10), the DELTREE command can be used to delete the whole directory. The deltree command is included in certain versions of Microsoft Windows and MS-DOS operating systems .
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 ...
Command line interpreters are programs that allow a user to interact with the underlying operating system by typing commands at a command prompt using a command line interface (CLI), in contrast to pointing and clicking a mouse in a graphical user interface (GUI).
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 ...
Here are some commands for the DOS, OS/2 and Microsoft Windows command prompt processor. The following command displays the contents of the file readme.txt. The program name is type and the argument is readme.txt. [6] type readme.txt The following command lists the contents of the current directory. The program name is dir, and Q is a flag ...