In addition to the clear underreporting of tasks within the pipelines as discussed above, the reporting of the bioinformatic tools and parameters used for those tasks cited in the papers was also very poor (Table 1). Only 21 of the 111 papers reported software name, version and parameters used for all of the bioinformatic tasks implemented, and 25 failed on all three counts (Fig. 4a). When considering the degree of underreporting by task (Fig. 4b), the most underreported software were used for some of the most perfunctory tasks (e.g. frequency filtering, length filtering, dereplication) that can be easily reproduced using many equivalent tools. Nonetheless, there remains relatively widespread underreporting, and this has remained unchanged over time (Fig. 5b).