MarginPolish¶
MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.
Environment Modules¶
Run module spider MarginPolish to find out what environment modules are available for this application.
System Variables¶
- HPC_MARGINPOLISH_DIR - installation directory
- HPC_MARGINPOLISH_BIN - executable directory