Additional file 2: Table S1. of HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

HiC-bench task implementation. The table summarizes how the pipeline tasks are implemented, which are the requirements for their execution and how they are handled by the pipeline-master-explorer script. The first column lists all the tasks performed by the pipeline ranging from alignment to annotation. The second column lists the input directory required for each task while the third one lists the parameter files. Certain tasks depend on the reference genome (human or mouse), thus the genome assembly acts as split variable (column 4). In some tasks, replicates can be grouped using the group variable (column 5). Pairwise comparisons between replicates or samples are also allowed using tuples (column 6). The last column lists the full pipeline-master-explorer command for each pipeline task. (XLSX 10 kb)

HiC-bench任务实现方案。本表格汇总了该分析流程的任务实现方式、执行所需前置条件，以及pipeline-master-explorer脚本对各任务的处理逻辑。第一列列出了该流程涵盖的全部任务，覆盖范围从序列比对（alignment）到基因组注释（annotation）。第二列列明了每项任务所需的输入目录，第三列则列出对应的参数文件。部分任务依赖参考基因组（reference genome，包含人类或小鼠），因此基因组组装版本作为拆分变量（第4列）。在部分任务中，可通过分组变量（group variable，第5列）对生物学重复样本（replicates）进行分组。此外，还可借助元组（tuples，第6列）完成生物学重复样本或不同样本间的两两比较。最后一列列明了每项流程任务对应的完整pipeline-master-explorer命令。（XLSX格式，文件大小10 KB）