Commands for running the pipeline

This file contains a list of the programs and parameter values we used for the bioinformatic analysis pipeline described in the paper. Note that the sequence of steps described in this file was designed to carefully evaluate the quality of sequencing data generated with a new library preparation method. For routine applications (where it may not be necessary to quantify the loss of data at each individual filtering step), several steps can be skipped, optimized or combined for a more streamlined pipeline.