rtcMakefile - A custom pipeline to search for retrocopies in genomes.
version 0.1 (latest)
$ source laucher.sh input.txt output_dir/
rtcMakefile aims to search for retrocopies in genomes or groups of genomes by mining its BAM files for abnormal alignments.
Just clone the GitHub repository from the command line:
$ git clone https://github.com/jlbuzzo/rtcMakefile.git
In order to properly run this pipeline, the user will need these programs installed:
- GNU make
- gawk
- Perl (5.26.2 or above)
Launching this pipeline is very straightforward. User needs to list all target
BAM files in a plain txt file with their absolute paths in the system
(e.g., inputs.txt). So, this:
$ source launcher.sh inputs.txt output_dir/
will save all the results for the files listed in the input file in the
outputs_dir directory.
NOTE 1: Before launch the processes, user must edit the opt.mk configuration
file to adjust its behavior to his system's context.
NOTE 2: The final part of this pipeline is very memory expensive!
- Coordination for the Improvement of Higher Level Personnel - CAPES
- Teaching and Research Institute from Sírio-Libanês Hospital - Group of Bioinformatics
- Fabio Navarro fnavarro@mochsl.org.br
- Thiago L. A. Miller tmiller@mochsl.org.br
- J. Leonel Buzzo lbuzzo@mochsl.org.br
- Gabriela Guardia gguardia@mochsl.org.br
- Fernanda Orpinelli forpinelli@mochsl.org.br
- Pedro A. F. Galante pgalante@mochsl.org.br
This software is Copyright (c) 2018 by Teaching and Research Institute from Sírio-Libanês Hospital.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007