Pairtools: From sequencing data to chromosome contacts
Fig 3
Benchmark of different Hi-C mapping tools for one mln reads in 5 iterations (data from [64]).
a. Runtime per tool and number of cores. The labels at each bar of the time plot indicate the slowdown relative to Chromap [58] with the same number of cores. b. Maximum resident set size for each tool and number of cores. c. Runtime per tool and number of cores compared to the runtime of the corresponding mapper (gray shaded areas). Labels at the bars reflect the percentage of time used by the mapper versus the time used by the pair parsing tool. d. Maximum resident set size for each tool and number of cores compared with that of the corresponding mapper. To make the comparison possible, the analysis for each tool starts with.fastq files, and the time includes both read alignment and pairs parsing. For pairtools, we tested the performance with regular bwa mem [34] and bwa mem2 [35], which is ~2x faster but consumes more memory. Note that for HiC-Pro, we benchmark the original version and not the recently-rewritten nextflow [65] version that is part of nf-core [66]. FANC, in contrast to other modular 3C+ pairs processing tools, requires an additional step to sort.bam files before parsing pairs that we include in the benchmark. For Juicer, we use the “early” mode. Chromap is not included in this comparison because it is an integrated mapper [58].