| Nelson et al. [15] | McClintock 2 |
---|---|---|
McClintock implementation | Bash | Python |
Workflow management | N.A. | Snakemake |
Dependency installation | Manual | Conda (automated) |
# Component methods | 6 | 12 (with extensibility) |
Read trimming and QC | N.A. | trimgalore module |
TE copy number estimation | N.A. | coverage module |
Output format | .BED | .VCF and .BED |
Summary report | .CSV | .CSV and .HTML (interactive) |
Reproducible simulation system | N.A. | Built-in (with documentation) |