MarginPolish¶

Description¶

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. While MarginPolish serves as a standalone assembly polisher, it is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-task RNN polisher HELEN. HELEN operates on images generated by MarginPolish.

Environment Modules¶

Run module spider marginpolish to find out what environment modules are available for this application.

Environment Variables¶

HPC_MARGINPOLISH_DIR - installation directory
HPC_MARGINPOLISH_BIN - executable directory

Categories¶

phylogenetics