CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.
- works with any number of scaffold assemblies in de-novo non-progressive fashion
- allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
- creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
- constructs a merged combined scaffold assembly
- provides an interactive framework for a visual comparative analysis of the given assemblies
- S. Aganezov and M. A. Alekseyev. “CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies”. BMC Bioinformatics 18:Suppl 15 (2017), 496. doi:10.1186/s12859-017-1919-y bioRxiv:10.1101/069153
CAMSA is developed using Python programming language and is compatible with both Python2 (2.7+) and Python3 (3.3+). This means CAMSA can be run on any modern operating system properly.
Note: only Linux and MacOS were tested extensively with respect to CAMSA installation and usage. If you want to use CAMSA on windows, please try to do so on your own (we have continuous integration setup on Windows platform as well, but no as detailed as on MacOS/Linux), and if you run into any problems – contact us.
The simplest way to install CAMSA is by using
pip. Open your terminal and execute the following command:
pip install camsa
For more details and other ways to install CAMSA please refer to the installation wiki page.
CAMSA expect as an input a set of different assemblies on the same set of scaffolds. Eash assembly must be represented as a set of assemblies points in TSF files, using the following format:
origin seq1 seq1_or seq2 seq2_or cw A1 s1 + s2 - ? A1 s2 - s3 + ? ...
CAMSA also provides a set of built-in scripts, that allow one to translate other scaffold assembly formats (i.e., FASTA, AGPv2.0, GRIMM, etc) into CAMSA format, and vice-versa (when possible). For more details please refer to the input wiki page.
CAMSA is very straightforward to use: installation process adds several executable scripts to your (python)path, which either execute CAMSA itself, or some of its utilities. Basic CAMSA usage is
run_camsa.py f1.camsa.points f2.camsa.points ... -o output_dir
This command would run CAMSA in both comparative and merging modes, producing extensive comparative assembly reports as well as a merged assembly. For more details on running CAMSA please refer to the usage wiki page.
For more details regarding both text-based and interactive reports please refer to the output wiki page.
A Cytoscape style, allowing one to work with exported Scaffold Assembly Graph in Cytoscape software can be downloaded from the following link
Contributing / Bug reports
Please submit any information about identified bugs to the corresponding GitHub bug tracker system.
Here are some of the screenshots of CAMSA report: