BlobToolKit – Interactive Quality Assessment of Genome Assemblies

Abstract

Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.

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References 46

1. 1.

   Altschul S., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.

   Not in our library10.1093/nar/25.17.3389

2. 2.

   Amid, C., B. T. F. Alako, V. Balavenkataraman Kadhirvelu, T. Burdett, J. Burgin et al., 2019 The European Nucleotide Archive in 2019. Nucleic Acids Res.

   Not in our library10.1093/nar/gkz1063

3. 3.

   Andreson R., Roosaare M., Kaplinski L., Laht S., Kõressaar T., 2019 Gene content of the fish-hunting cone snail Conus consors. bioRxiv. 590695

   Not in our library10.1101/590695

4. 4.

   Arakawa K., 2016 No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc. Natl. Acad. Sci. USA 113: E3057

   Not in our library10.1073/pnas.1602711113

5. 5.

   Artamonova I. I., Lappi T., Zudina L., and Mushegian A. R., 2015 Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe. Environ. Microbiol. 17: 2203–2208.

   Not in our library10.1111/1462-2920.12854

6. 6.

   Bailey J. A., Gu Z., Clark R. A., Reinert K., Samonte R. V., 2002 Recent segmental duplications in the human genome. Science 297: 1003–1007.

   Not in our library10.1126/science.1072047

7. 7.

   Bakker F. T., Lei D., Yu J., Mohammadin S., Wei Z., 2016 Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline. Biol. J. Linn. Soc. Lond. 117: 33–43.

   Not in our library10.1111/bij.12642

8. 8.

   Bohlin J., Snipen L., Hardy S. P., Kristoffersen A. B., Lagesen K., 2010 Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics 11: 464

   Not in our library10.1186/1471-2164-11-464

9. 9.

   Buchfink B., Xie C., and Huson D. H., 2015 Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12: 59–60.

   Not in our library10.1038/nmeth.3176

10. 10.

    Challis, R. J., S. Kumar, K. Dasmahapatra, C. D. Jiggins, and M. Blaxter, 2016 Lepbase: the Lepidopteran genome database. bioRxiv 056994

    Not in our library10.1101/056994

11. 11.

    Crotti E., Rizzi A., Chouaia B., Ricci I., Favia G., 2010 Acetic acid bacteria, newly emerging symbionts of insects. Appl. Environ. Microbiol. 76: 6963–6970.

    Not in our library10.1128/aem.01336-10

12. 12.

    Delmont T. O., and Eren A. M., 2016 Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ 4: e1839

    Not in our library10.7717/peerj.1839

13. 13.

    Dunning Hotopp J. C., Clark M. E., Oliveira D. C., Foster J. M., Fischer P., 2007 Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317: 1753–1756.

    Not in our library10.1126/science.1142490

14. 14.
    A field guide to whole‐genome sequencing, assembly and annotation · 2014

    No notice
15. 15.
    Anvi’o: an advanced analysis and visualization platform for ‘omics data · 2015

    No notice
16. 16.

    Florea L., Di Francesco V., Miller J., Turner R., Yao A., 2005 Gene and alternative splicing annotation with AIR. Genome Res. 15: 54–66.

    Not in our library10.1101/gr.2889405

17. 17.

    Galtier N., Piganeau G., Mouchiroud D., and Duret L., 2001 GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159: 907–911.

    Not in our library10.1093/genetics/159.2.907

18. 18.

    Genome 10K Community of Scientists, 2009 Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J. Hered. 100: 659–674.

    Not in our library10.1093/jhered/esp086

19. 19.

    Gibbs R. A., Weinstock G. M., Metzker M. L., Muzny D. M., Sodergren E. J., 2004 Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493–521.

    Not in our library10.1038/nature02426

20. 20.

    Jarvis E. D., Mirarab S., Aberer A. J., Li B., Houde P., 2014 Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320–1331.

    Not in our library10.1126/science.1253451

21. 21.

    Köster J., and Rahmann S., 2018 Snakemake-a scalable bioinformatics workflow engine. Bioinformatics 34: 3600

    Not in our library10.1093/bioinformatics/bty350

22. 22.

    Kumar S., and Blaxter M. L., 2011 Simultaneous genome sequencing of symbionts and their hosts. Symbiosis 55: 119–126.

    Not in our library10.1007/s13199-012-0154-6

23. 23.
    Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots · 2013

    No notice
24. 24.

    Laetsch D. R., and Blaxter M. L., 2017 BlobTools: Interrogation of genome assemblies. F1000 Res. 6: 1287

    Not in our library10.12688/f1000research.12232.1

25. 25.

    Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., 2001 Initial sequencing and analysis of the human genome. Nature 409: 860–921.

    Not in our library10.1038/35057062

26. 26.

    Lewin H. A., Robinson G. E., Kress W. J., Baker W. J., Coddington J., 2018 Earth BioGenome Project: Sequencing life for the future of life. Proc. Natl. Acad. Sci. USA 115: 4325–4333.

    Not in our library10.1073/pnas.1720115115

27. 27.

    Li H., 2018 Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34: 3094–3100.

    Not in our library10.1093/bioinformatics/bty191

28. 28.

    Li H., and Durbin R., 2010 Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589–595.

    Not in our library10.1093/bioinformatics/btp698

29. 29.
    Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage. · 2011

    Not checked
30. 30.

    López-García P., Eme L., and Moreira D., 2017 Symbiosis in eukaryotic evolution. J. Theor. Biol. 434: 20–33.

    Not in our library10.1016/j.jtbi.2017.02.031

31. 31.
    Unexpected cross-species contamination in genome sequencing projects · 2014

    No notice
32. 32.

    Morgulis A., Gertz E. M., Schäffer A. A., and Agarwala R., 2006 WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22: 134–141.

    Not in our library10.1093/bioinformatics/bti774

33. 33.

    Mural R. J., Adams M. D., Myers E. W., Smith H. O., Miklos G. L. G., 2002 A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661–1671.

    Not in our library10.1126/science.1069193

34. 34.

    Oldeschulte D. L., Halley Y. A., Wilson M. L., Bhattarai E. K., Brashear W., 2017 Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3 (Bethesda) 7: 3047–3058.

    Not in our library10.1534/g3.117.043083

35. 35.

    Pruitt K. D., Tatusova T., and Maglott D. R., 2005 NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33: D501–D504.

    Not in our library10.1093/nar/gki025

36. 36.

    Romiguier J., Ranwez V., Douzery E. J. P., and Galtier N., 2010 Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 20: 1001–1009.

    Not in our library10.1101/gr.104372.109

37. 37.

    Sackton T. B., Grayson P., Cloutier A., Hu Z., Liu J. S., 2019 Convergent regulatory evolution and loss of flight in paleognathous birds. Science 364: 74–78.

    Not in our library10.1126/science.aat7244

38. 38.

    Salinas J., Matassi G., Montero L. M., and Bernardi G., 1988 Compositional compartmentalization and compositional patterns in the nuclear genomes of plants. Nucleic Acids Res. 16: 4269–4285.

    Not in our library10.1093/nar/16.10.4269

39. 39.
    Reagent and laboratory contamination can critically impact sequence-based microbiome analyses · 2014

    No notice
40. 40.
    Serendipitous discovery of Wolbachia genomes in multiple Drosophilaspecies · 2005

    No notice

Cited by papers we hold 9

• Rapid and sensitive detection of genome contamination at scale with FCS-GX · 2024
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• Quality assessment of gene repertoire annotations with OMArk · 2024
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• Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life · 2023
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• compleasm: a faster and more accurate reimplementation of BUSCO · 2023
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• Sequence locally, think globally: The Darwin Tree of Life Project · 2022
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• The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens [version 1; peer review: 2 approved] · 2021
  Not checked
• The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758) [version 1; peer review: 3 approved] · 2021
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• Significantly improving the quality of genome assemblies through curation · 2021
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• Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel · 2020
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