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I use SOAPdenovo2 to assemble a large genome (4.8G) using ~20X paired-end reads. The total length of contig sizes is 6.3G while total length of scaffolds is 2.7G. Note that this is a haploid genome, so there is no issue of heterozygosity for scaffolding.

I am wondering what happened during the scaffolding procedure? How comes that sum of scaffolds is so much smaller than sum of contigs?

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    $\begingroup$ Scaffolding probably throws out small contigs. Without being an expert in soapdenovo2, I would first bwasw the contigs to he scaffolds to see which sequence looks "lost". $\endgroup$
    – Manuel
    Jun 4 '17 at 14:34
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Something else that could be happening is that contigs that are being collapsed into "heterozygous" groups. This would be a particular problem when a genome has a substantial amount of repeated sequence. Digging deep into the supplementary information of the SOAPdenovo2 paper, I've found the following information:

In SOAPdenovo2, heterozygous contig pairs are recognized by utilizing the information of contig depth and the locality of contig. The recognized heterozygous contig pairs should obey the following rules: 1) the similarity between contigs should be high enough, for example, ≥ 95%; 2) the depth of both contigs should be near half of the average depth or all contigs, complying Poisson distribution; 3) the two contigs should be located adjacently in a scaffold and have no relationship to each other inferred by paired-end reads information. The normal contigs neighboring the heterozygous regions, if they exist, could be connected to both of the heterozygous contig pairs (H1 and H2). Only the contig with relatively higher depth in a heterozygous contig pair were kept for scaffolding. The method reduces the influence of genome heterozygosity on final scaffold length. All heterozygous contig pairs were outputted to a file to facilitate further analysis. However, the trade-off of this method is that it might incorrectly remove paralogous contigs. This problem could be relieved by a gap-filling procedure while the removed copy of paralogous contigs would be represented by gaps during scaffolding.

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  • $\begingroup$ Nice. However, this can't be a complete answer, because of "2) the depth of both contigs should be near half of the average depth or all contigs, complying Poisson distribution;". Because in the OP's case the reduction of size is from 6.3G to 2.7G, which means that more than a half of contigs would be coverage outliers. $\endgroup$
    – Kamil S Jaron
    Jun 5 '17 at 10:30
  • $\begingroup$ That would be true for a diploid genome that has a low amount of repeats, but if there's substantial gene duplication (as happens with very large genomes), then the collapsed sequence will be a lot smaller. However, I'm not excluding other factors, just pointing out that this is one of the possible explanations. $\endgroup$
    – gringer
    Jun 5 '17 at 10:36
  • $\begingroup$ I just wanted to point out, that there got to be something else as well given those numbers... $\endgroup$
    – Kamil S Jaron
    Jun 5 '17 at 10:59
  • $\begingroup$ Maybe also the filtering of small contigs as @manuel says. $\endgroup$
    – Kamil S Jaron
    Jun 5 '17 at 21:25
  • $\begingroup$ Nice. I see there are at least a few factors we agreed: low coverage of contigs, small contigs, also possible high gene duplication levels. I also have 3 mate-pair libraries with 10X each, will use them for scaffolding and gap closer. Hopefully this will tell us a bit more on this issue. i will keep you update. $\endgroup$ Jun 6 '17 at 5:54

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