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Table 3 Performance of the LAST+MEGAN-LR pipeline

From: MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

Step Input Output Runtime Memory
PacBio reads on HMP mock community
Align Reads file (1.5 GB) MAF file 119 min 23 GB
Convert MAF file (49 GB) DAA file 29 min 5 GB
Classify DAA file (4.2 GB) Meganized DAA file (4.5 GB) 6 min 5 GB
PacBio reads on Singer et al. mock community
Align Reads file (56 MB) MAF file 10 min 22 GB
Convert MAF file (8.9 GB) DAA file 5 min 5 GB
Classify DAA file (197 MB) Meganized DAA file (415 MB) 1 min 5 GB
Nanopore reads on HMP mock community
Align Reads file (191 MB) MAF file 10 min 22 GB
Convert MAF file (6.1 GB) DAA file 3 min 5 GB
Classify DAA file (553 MB) Meganized DAA file (644 MB) 1 min 5 GB
Anammox data
Align Reads file (336 MB) MAF file 31 min 24 GB
Convert MAF file (8.5 GB) DAA file 4 min 5 GB
Classify DAA file (371 MB) Meganized DAA file (500 MB) 2 min 5 GB
Cheese data
Align Reads file (5.1 GB) MAF file 251 min 24 GB
Convert MAF file (93 GB) DAA file 90 min 10 GB
Classify DAA file (3.1 GB) Meganized DAA file (3.5 GB) 5 min 10 GB
  1. For each of five long read datasets, we report the wall-clock time and main memory required by LAST to align against the NCBI-nr database, for MEGAN to convert the LAST MAF output files into DAA format, and then for MEGAN to classify the reads so as to meganize the DAA file, respectively. The computations were performed on a Linux server with 32 cores and 512GB memory