- Breakpoints via assembly
- Quick installation
- Running BRASS
- Docker, Singularity and Dockstore
Breakpoints via assembly
BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.
There are several stages the main component being:
- Collect read-pairs where both ends map but NOT marked as properly-paired.
- Perform grouping based on mapped locations
- Run assembly
- Annotate with GRASS
Skipping all external dependencies
If you want to only install the core of BRASS (C and perl wrappers) and use existing versions of tools from your path run as:
./setup.sh path_to_install_to 1
Skipping exonerate install
Central install via package manager of 2.2.0 is adequate. To skip just exonerate install run:
./setup.sh path_to_install_to 2
- The C++ code (within this package) requires the presence of
pstreams.h(and associated development libraries). This is not handled by the
Each of these has it's own dependencies.
A large number of R packages are required to run BRASS. To facilitate the install process there is
Rsupport/libInstall.R that can be run to build these for you. See this file for the list
Alternatively you can run:
cd Rsupport ./setupR.sh path_to_install_to
1 to the command will request a complete local build of
Other tools that need to be in path
- If not done failures due to absence of
ssearch36is the only program required.
- If not done failures due to absence of
Tools installed by setup.sh
setup.sh to install these dependencies. Setting the environment variable
CGP_PERLLIBS allows you to to append to
PERL5LIB during install. Without this all dependancies
are installed into the target area.
setup.sh will not use
Please be aware that this expects basic C compilation libraries and tools to be available.
This package includes a reference implementation which handles all of the linking together of steps.
Please see the
-m options of
brass.pl for full usage information.
It can be run in a couple of ways:
- Fire and forget
- Execute on a single host with multiple cores (or 1 if that's all you have)
- Some efficiency overhead as some steps aren't parallel
- Farm style
- Requires 2 extra parameters in the initial command
-helpfor further details
BRASS has primarily been written to work with BWA mapped data. You are likely to get the most useful output from BWA-mem.
Please be aware that paired-end libraries where properly-paired reads are heavily overlapped are unlikely to produce good results.
Additional mapping information
BRASS requires accurate information regarding the insert size distribution and expects to find a
*.bam.bas file co-located with the
*.bam's. These can be generated by the
program included in the PCAP-core project.
If you use
bwa_mem.pl to map your data (same repository) then this file is generated
automatically for you.
Docker, Singularity and Dockstore
There is a pre-built image containing this codebase on quay.io.
- dockstore-cgpwgs: Contains additional tools for WGS analysis.
This was primarily designed for use with dockstore.org but can be used as normal containers.
The docker images are know to work correctly after import into a singularity image.
Copyright (c) 2014-2018 Genome Research Ltd. Author: CASM/Cancer IT <email@example.com> This file is part of BRASS. BRASS is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. 1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’."