Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are Illumina WGS reads, Oxford Nanopore, PacBio, and 10X reads available for download at high coverage depth. In addition, there are pre-aligned bam files and verified variant calls.

Is there any aggregation of similar robust single-individual sequencing resources for non-human, non-mammalian metazoan species? The only way I can consider finding such resources at the moment is going through SRA projects one at a time and hoping for the best.


In addition I would like to add "Vectorbase", the curator "Dan" is a good guy (I forget his surname right now) and it's a good team. However, please read my rather somber assessment of arthropod genomics first.

We appear to be talking about lower metazoans, e.g. not protists, or yeasts (the latter I suspect are really good for your question). I don't know anything about worms.

Its important to understand that arthropods are several (soccer) divisions lower than mammals in terms of the question you are asking, except for two model organisms.

Flybase, Drosophila melanogaster is the most important species for your purposes. The second most important species within the Class Insecta will be Anopheles gambiae (malaria mosquito).

Personally I would stick to the main players because overall whilst there are a lot of insect genomes (because there are a lot of insects), their genomes remain rough because of the difficulties in assembly and requirement to physical mapping their genomes in comparison to their genome size. Also except for D. melenogaster the (incredible) tardiness in producing a draft genome. For example the idea of PacBio is in its infancy for many entomologists: and this would help them a lot in assembling their genomes correctly. I agree things have picked a lot recently, but I remain a skeptic.

Within the arthropods I would be very surprised if the crustacea, myriapods or Chelicerata (e.g. spiders) were in better condition than hexapods.

If you are interested in protists certainly Plasmodium falciparum (African malaria) has the sort of information you seek (Plasmodb).

Summary I don't want to discourage you, insects are great, but you need to be selective if you are from a human/mammalian genetics background.

  • $\begingroup$ Does FlyBase or Plasmodb actually have the sort of data GIAB offers? High quality reads files and validated variants for those reads? And there are draft (and not so draft) genomes for dozens of insects by now. I was involved in the 12 Drosophilas paper, more than a decade ago, and have worked with A. gambiae, A. aegypti, T. castaneum, A. melifera among others. I've since left the field of comparative genomics, but I am surprised at your claim of a scarcity of genomes given there were already several available a decade ago. Have they since stopped working on them? $\endgroup$
    – terdon
    Feb 25 '19 at 18:19
  • $\begingroup$ Wait, wait ... . I'm not claiming scarcity of genome - no way - (there are lots of insect genomes), I am claiming quality of genome will still be absent. Drosophila is an exception, with D. melanogaster exceptional quality. For example, physical mapping against the polytene chromosomes was certainly lacking for most insects but is easily doable and would really help assembly. I was in on tsetse and a hemipteran genome. GIAB I don't keep up but I'd be surprised if melanogaster was not up to this standard. $\endgroup$
    – M__
    Feb 25 '19 at 18:54
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    $\begingroup$ Ah, OK, that makes more sense. It was the "tardiness in producing a draft genome" that threw me. As for GIAB, it isn't so much the quality as the type of data. They offer raw reads and.or aligned bam files and, most importantly, a "truth set" of variants that should be found in those reads. So it's a great (well, it's the only one, anyway) tool for validating variant calling pipelines. I don't know if such a dataset is available for non-human organisms. $\endgroup$
    – terdon
    Feb 25 '19 at 19:12
  • $\begingroup$ @MichaelG. I work with marine invertebrate metazoans! Thanks for your answer. $\endgroup$
    – conchoecia
    Feb 26 '19 at 17:11

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