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Table 4 Metrics of assemblies of the c22 dataset

From: Readjoiner: a fast and memory efficient string graph-based sequence assembler

Assemblathon metrics RJ SGA Edena LEAP
Number of contigs 120712 231594 120462 113428
Genome size (bp) 34894545 34894545 34894545 34894545
Total contigs length 45667531 55880641 44737441 43099113
- as  % of genome 130.87 160.14 128.21 123.51
Mean contig size 378.32 241.29 371.38 379.97
Median contig size 132 101 120 117
Longest contig 41352 41352 41352 39379
Shortest contig 102 100 100 101
Contigs > 500 bp 13467 (11.16%) 13416 (5.79%) 13439 (11.16%) 13430 (11.84%)
Contigs > 1 Kbp 8700 (7.21%) 8684 (3.75%) 8696 (7.22%) 8578 (7.56%)
Contigs > 10 Kbp 264 (0.22%) 264 (0.11%) 264 (0.22%) 228 (0.20%)
N50 1614 815 1699 1617
L50 5684 10118 5416 5488
NG50 2737 2739 2733 2461
LG50 3120 3113 3121 3429
Plantagora metrics RJ SGA Edena LEAP
Covered Bases 34343945 34357693 34300114 12968118
Ambiguous Bases 159997 154584 182952 696334
Misassemblies 4 4 4 3693
Misassembled Contigs 4 4 4 2344
Misassembled Contig Bases 1283 417 1245 2797710
SNPs 104 125 120 46270
Insertions 5 2 1 2403
Deletions 43 23 28 5187
Positive Gaps 2679 2471 2925 26495
Internal Gaps 0 0 0 21
External Gaps 2679 2471 2925 26474
- total length 547408 558921 589979 19064103
- average length 204 226 202 720
Negative Gaps 110888 218908 110811 18198
Internal Overlaps 0 0 0 17
External Overlaps 110888 218908 110811 18181
- total length −10247647 −20078971 −9424823 −1859835
- average length −92 −92 −85 −102
Redundant Contigs 864 1158 607 6329
Unaligned Contigs 3262 4686 3221 60563
- partial 18 57 21 3252
- total length 462668 599320 447922 27666823
Ambiguous Contigs 2631 3876 2619 799
- total length 369284 483895 366418 93102
  1. Metrics of the assemblies of the dataset c22 as delivered by Readjoiner (RJ), SGA, Edena and LEAP ( min =45). The metrics are explained in [26] and in [28].