Review for "Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes"

Completed on 25 May 2018 by Marcel Schulz & Dilip Durai .

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Comments to author

In the manuscript, Johnson et al have reassembled RNA-seq data from 678 samples generated from MMETS Project using a pipeline, which follows the Eal Pond mRNA seq protocol. The pipeline (DIG) starts by quality trimming the data followed by digital normalization and assembly using the Trinity assembler. The authors have compared their re-assemblies against assemblies generated from the method suggested by the National Center for Genome Resource (NCGR). For comparison, they have used difference evaluation metrics like Conditional Reverse Best BLAST (CRBB), BUSCO scores, annotation using the Dammit pipeline and ORF content in the assembly. They argued that their pipeline is able to provide additional biologically meaningful content as compared to the NCGR pipeline. While the work overall is quite interesting and the large set of assemblies appear useful, I feel that there are some improvements and clarifications necessary:

Major comments:

1) The core reason behind the observation that DIG pipeline being better than the NCGR pipeline is not clear. It might be due to the core algorithm behind the assembler used by the pipelines (DIG using Trinity and NCGR uses AbySS). But this should be explained in more detail why their pipeline performs better. For example, is the performance increase linked to sequencing coverage of the read data sets? Or transcriptome complexity of the sample? Or is it the fact that the NCGR pipeline seems to use a custom build pipeline that uses multi-kmer ABySS but not the de novo transcriptome assembler trans-ABySS, which may be more suited?

2) The other major difference between the pipelines is the additional step of digital normalization which DIG uses. Normalization generally removes kmer information, which affect the overall assembly. It is not clear why normalization in case of DIG should improve the assemblies. Normally the expectation would not that the digital normalization leads to an improvement. So I assume the authors do it simply to reduce the computational costs of the many assemblies, which is plausible but should be stated.

Also, Trinity by default performs in-silico normalization. So, the additional normalization step is redundant. Is the option for normalization switched off in the assembler. If yes, the authors should comment on why they are using Diginorm instead of using Trinity's built-in normalization, is there any indication that this works better for the assemblies they have done?

3) It is not clear which version of NCGR assemblies ("nt" or "cds") the authors used for calculating the mean ORF% in Table 1. If they have used the "nt" version, then the number can be misleading. The "cds" version of the NCGR assemblies contains contigs that have been predicted to show coding potential and hence might have a higher mean ORF content (as this is computed as percentages). I suggest the authors compare the mean ORF% content of the two NCGR version against the assemblies generated using DIG for full transparency and then discuss the differences regarding these two NCGR version and their assemblies.

4) I think the line plots used in the paper can be improved, because it is hard to quantify the amount of overlapping lines. For example I think that Figure 2A, 3A,5A,5C are probably more easy to interpret when made as a scatterplot, e.g. Fig2A where the number of contigs is compared between NCGR and DIB assemblies.

5) I would not say that the distribution in Figure 2c looks like a Normal distribution as the right tail is much heavier than the left one. If you want to make that statement, use a test of normality, however I feel this is not important for the paper.

Minor comments:

-Typo in reference 25 .. de ovo assembly ..

-line 336: I was not able to understand what the (see op-ed Alexander et al. 2018 ) refers to, as there is no such reference in the bibliography and no footnote