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Table 1 Summary statistics of aligning PacBio/ONT reads to short-read assembly graphs (constructed by SPAdes with kmer size equal to 77)

From: SPAligner: alignment of long diverged molecular sequences to assembly graphs

Aligner MR(%) AI (%) T (h:m) M (Gb)   MR(%) AI (%) T (h:m) M (Gb)
E. coli PacBio   E. coli ONT
vg 29 90 00:41 4.1   58 88 00:33 3.3
GraphAligner 85.3 86.7 00:01 0.1   82.2 86.1 00:01 0.2
GA try-all-seeds 86 86.6 00:25 0.3   83.6 86 01:43 4.8
SPAligner 88.3 86.5 00:04 0.3   86.6 86.1 00:03 0.3
S. cerevisiae PacBio   S. cerevisiae ONT
vg 15 90 28:03 91   70 47 42:59 85
GraphAligner 53.7 86.5 00:01 0.2   65.7 81.1 00:01 0.2
SPAligner 56.5 85.9 00:38 0.7   61.6 82.1 00:16 0.6
C. elegans PacBio   C. elegans ONT
vg 10 91 76:26 306   15 89 60:58 309
GraphAligner 84.1 86.8 00:03 1.8   63.6 86.6 00:03 1.8
SPAligner 84.6 86.5 01:06 1.2   66 86.4 00:34 1.3
  1. Every dataset consists of 10k reads longer than 2Kbp (except E. coli ONT dataset with 7k reads of appropriate length). All runs performed in 16 threads. Due to high fragmentation of assembly graph resulting from available C. elegans Bristol N2 Illumina sequencing data, we used simulated Illumina reads to obtain C. elegans assembly graph