Tips for running ntLink

Optimizing k/w for ntLink step

• The default k (k) and w (w) values for ntLink generally work well, but (depending on your input data) you may get better results by tuning these parameters
• Generally, we suggest setting the k-mer and window size to values in these approximate ranges:
  • k (k-mer size): 24-40
  • w (window size): 100-500
• These values can be optimized using a grid search
  • For example, trying all combinations of k-mer sizes 24, 32, 40 and window sizes 100, 250, 500

Information about threads

• The minimizer generation step of ntLink (indexlr) is multi-threaded
  • This step uses a maximum of 5 threads

Cleaning up intermediate files

• ntLink provides a couple of options for automatically cleaning up intermediate files from a run
  • For ntLink, you can specify the additional targets clean and/or extra_clean
    • These still clean-up intermediate files, with extra_clean being more aggressive, and basically only leaving the final output scaffolds file
  • For ntLink_rounds, you can also specify the additional target clean
    • When running rounds, the clean and extra_clean targets for ntLink are automatically specified