For each of the bioinformatic tasks identified across the papers, we calculated (i) the number of papers implementing the task, (ii) the task’s relative position within the pipelines, (iii) the information reported on the software, version and parameters used, and (iv) the homogeneity in the software tools used to implement the task. We assessed homogeneity by calculating two indices, the software homogeneity rate and the software dominance rate (see Fig 5). Finally, we also summarised temporal trends in both the reporting and software heterogeneity of each task.