GROMACS dcTMD free energy calculation

Perform an ensemble of targeted MD simulations of a user-specified size using the GROMACS PULL code and calculate dcTMD free energy and friction profiles for the resulting dissocation pathway. Note that pathway separation is not performed by the workflow; the user is responsible for checking the ensemble themselves.

The input protein (PDB) and ligand (SDF) files provided are parameterized by the 'Protein-ligand complex parameterization' subworkflow.

Note ...

Protein-ligand complex parameterization

Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS.

This is a simple workflow intended for use as a subworkflow in more complex MD workflows. It is used as a subworkflow by the GROMACS MMGBSA and dcTMD workflows.

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.