A KBase module generated by the KBase SDK.
MaSuRCA References:
https://academic.oup.com/bioinformatics/article/29/21/2669/195975/The-MaSuRCA-genome-assembler
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt476
ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/
The MaSuRCA Quick Start Guide is available here:
https://github.com/alekseyzimin/masurca
ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf
General steps to run the MaSuRCA assemblers:
First, create a configuration file which contains the location of the compiled assembler (the
executable), data and assembly parameters.
(The config file consists of two sections: DATA and PARAMETERS. Each section concludes with END statement.
User should copy the sample config file to the directory of choice for running the assembly and
then modify it according to the specifications of the assembly project.)
Second, run the 'masurca' script which will generate from the configuration file a shell script
'assemble.sh', which is the main driver of the assembly.
(Once you’ve created a configuration file, use the ‘masurca' script from the MaSuRCA bin directory
to generate the 'assemble.sh' shell script that executes the assembly:
$ /install_path/ MaSuRCA-X.X.X/bin/masurca config.txt)
Finally, execute the script 'assemble.sh' to assemble the data.
For more help on how to modify, register and deploy the example to KBase, see the KBase SDK documentation.