How should one choose between transposase-based library preparation and mechanical fragmentation-based library preparation reagents?

The library complexity requirements for ATAC-seq and low-input whole-genome sequencing are different, so it is recommended to choose them separately. The standard for ATAC-seq is the Tn5 transposase method; do not use mechanical fragmentation, as it will disrupt open chromatin signals. When selecting domestic transposase reagents, confirm that they are an ATAC-specific system that includes nuclear permeabilization, transposition reaction, and purification steps; do not buy bare Tn5 enzyme only. For low-input whole-genome sequencing, if the sample DNA amount is sufficient and there are high requirements for uniformity and structural variant detection, the library complexity of mechanical fragmentation plus end repair is usually more stable, but the cost is higher and the input requirement is also higher. Within a budget of 80 yuan/reaction, the domestic transposase method is feasible for ATAC-seq; if WGS is also to be covered, it is best to first perform small-sample sequencing to validate the unique mapping and duplication rates.

For issues like stability and batch-to-batch variation, imported products generally offer more consistent enzyme activity quality control, but the per-reaction cost can rarely be brought below 80 yuan. Several domestic suppliers of transposase are more price-friendly, and you can request trial samples for parallel validation. I recommend that during validation you do not look only at library concentration; be sure to take 1–2 samples for shallow sequencing and compare library complexity, duplication rate, and insert size distribution. For ATAC-seq, also check the TSS enrichment score, and for WGS, check coverage uniformity. To keep the budget at 80 yuan, you must include adapters, indexes, magnetic beads, and purification steps in the calculation. Some domestic kits have a cheaper standalone enzyme, but if the matching purification magnetic beads must be purchased separately, the budget will be exceeded. When selecting a product, ask clearly whether the full set of components is included, and require the supplier to provide enzyme activity QC data for the transposase.

My lab has been using the transposase method for ATAC-seq for two years, and we have switched between domestic and imported products. My personal impression is: for ATAC-seq with the transposase method, there is no need to get hung up on mechanical fragmentation; the key is to optimize the transposition reaction time and the number of nuclei. Over-transposition will cause fragment shortening, and complexity will instead decrease. For small-scale whole-genome sequencing, I still use sonication fragmentation plus end repair, because the transposase method is slightly worse than mechanical fragmentation in controlling GC bias and coverage uniformity, especially in low-coverage regions. Within a budget of 80 yuan, domestic transposase reagents can cover a single ATAC-seq reaction, but for WGS, keeping the entire workflow within 80 yuan is quite tight unless the sample number is small and the cycle number is low. In terms of stability, it is recommended to run two replicates from the same batch, check the main fragment peak and qPCR yield differences, and proceed to samples only after the differences are within an acceptable range.