Mem-based pangenome indexing for k-mer queries

Table 4 VGP index resource

Method	Time	CPU %	Memory (GB)
PanKmer	15:48:00	99%	273.52
KMC3-M	00:07:50	740%	12.02
KMC3-C	01:27:15	173%	12.03
MEMO-M	13:45:24	839%	278.85
MEMO-C	14:37:56	799%	278.85

Time (hours:minutes:seconds), CPU %, and peak memory usage as output from /usr/bin/time. PanKmer was run in 20 rounds with 1 thread and gzip-level 6. KMC3 was run with 48 threads [default, max no. of CPU cores] and 12 GB max RAM. MEMO index creation relies on MONI to find MSs. MONI was run with 8 threads for the build and MS finding steps

ISSN: 1748-7188