LPMX: a pure rootless composable container system

BMC Bioinformatics

Table 2 Running time for bwa-mem2 (ver 2.2.1), samtools (ver 1.13 with htslib) and GATK (ver 4.2.1.0 with HTSJDK ver 2.24.1 Picard ver 2.25.4) with the same dataset on the bare host and LPMX

For GATK, we record the time for HaplotypeCaller. During the experiment, the shared file server is moderately loaded. The time difference between the bare host and LPMX can be explained largely by varying loads of the central shared file system over time, not by the performance overhead of LPMX. Data files and read files are available here (https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002, https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/). The scripts are available here (https://github.com/JasonYangShadow/experiment_attachments)

ISSN: 1471-2105