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Fig. 3 | Genome Biology

Fig. 3

From: OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees

Fig. 3

Boosting assembly contiguity and correctness with OPERA-LG. a, b Scaffold contiguity and correctness for various scaffolders on different genomes starting from common sets of contigs (generated by SOAPdenovo). The final assemblies were only corrected for scaffold errors. Results for BESST and SOPRA were comparable to those for SSPACE and are reported in Additional file 1: Table S2. c, d Corresponding overall assembly metrics for various assembly pipelines (that were provided all read libraries as input). The final assemblies were corrected for both contig and scaffold errors to allow for a fair comparison. Arrows highlight fold improvement in corrected N50 using OPERA-LG. ALLPATHS-LG analysis on the H. sapiens dataset had an abnormal exit after >10 days of runtime but appears to have produced a valid assembly. e, f Overall assembly contiguity as a function of mate-pair libraries and sequencing depth, provided as input. Results shown are for the C. elegans dataset and are qualitatively similar for other datasets as well (data not shown)

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