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README_makeTree.md

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makeTree user manual

Reads a fasta file, creates a tree structure of a predefined depth DEPTH and saves it to a file.

NOTE: computing a tree from a fasta file is very memory intensive. The program will not compute a tree if the length of the sequences in the fasta file exceeds 10 MB.

Running the program

Usage C executable (in folder bin):

Usage: makeTree -f|--fasta <FASTA_INPUT> -l|--depth <DEPTH> 
-o, --output <OUTPUT_FILE> Reads a *fa file, constructs a tree of 
depth DEPTH and saves it compressed in OUTPUT_FILE.
Options: 
 -v, --version Prints package version.
 -h, --help    Prints help dialog.
 -f, --fasta   Fasta input file of potential contaminations. Mandatory option.
 -l, --depth   depth of the tree structure.
 -o, --output  Output file. If the extension is not *gz, it is added. Mandatory option.

Output description

Compressed file containing the tree structure. For further details, read the Doxygen documentation of the file tree.c, function save_tree.

Contributors

Paula Pérez Rubio

License

GPL v3 (see LICENSE.txt)