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Table 4 Benchmarking results for real Oxford Nanopore reads. HC haplotype coverage, ER error rate (mismatches + indels + N’s), MC misassembled contigs proportion. NGA50 is labeled with ’-’ if the uniquely aligned blocks cover less than half of the reference length. Note that the metrics for the SARS-CoV-2 real sample in this table are not necessarily correct but for reference only, because the ground truth is unknown and we only used the sequence of Wuhan-Hu-1 (NC_045512) as the truth for comparison. † Strainline consensus as reference, using reads corrected by Strainline error correction. * Sometimes NGA50 still reports a value (5456 bp) even if HC <50% because contigs have overlaps (See https://github.com/ablab/quast/discussions/ 174 for the detailed explanation)

From: Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

 

#Contigs

HC (%)

N50 (bp)

NGA50 (bp)

ER (%)

MC(%)

5-strain PVY mixture

Strainline

7

97.9

9538

9548

0.956

0.0

Canu

3

39.9

9665

5456*

0.105

0.0

Wtdbg2

2

26.0

7632

-

4.931

0.0

SARS-CoV-2 (SRP250446)

Strainline

1

99.9

29,565

29,565

0.832

0.0

Canu

-

-

-

-

-

-

Wtdbg2

1

65.8

19,405

19,396

1.542

0.0

CliqueSNV †

1

99.9

29,565

29,565

0.859

0.0