| Master | Develop |
|---|---|
 |
 |
- Breakpoints via assembly
- Quick installation
- Pre-requisites
- Running BRASS
- Input
- Docker, Singularity and Dockstore
- LICENCE
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
- Filter
- Run assembly
- Annotate with GRASS
./setup.sh path_to_install_to
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
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 thesetup.shscript.
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
a script Rsupport/libInstall.R that can be run to build these for you. See this file for the list
of packages.
Alternatively you can run:
cd Rsupport
./setupR.sh path_to_install_to
Appending 1 to the command will request a complete local build of R (3.1.3).
- FASTA
- If not done failures due to absence of
ssearch36will occur. ssearch36is the only program required.
- If not done failures due to absence of
Please use 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 PERL5LIB directly.
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 -h and -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
- See
-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.
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 bam_stats
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.
There are pre-built images containing this codebase on quay.io.
- brass
- Just this repo and any dependencies.
- dockstore-cgpwgs
- Contains additional tools for WGS analysis
- This was primarily designed for use with dockstore.org but can be used as normal container
The docker images are know to work correctly after import into a singularity image.
Copyright (c) 2014-2019 Genome Research Ltd.
Author: CASM/Cancer IT <[email protected]>
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’."
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent