Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible filtering.
BlobToolKit Viewer allows browser-based interactive visualisation and filtering of preliminary or published genomic datasets even for highly fragmented assemblies.
Multiple views and data export options dynamically update as filter parameters and selections are modified (Figure 1).
We are running the BlobToolKit pipeline (Figure 2) on all public (INSDC registered) eukaryote genome assemblies and making the results available here.
1 Kumar et al. 2013. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Frontiers in Genetics, 4:237
2 Laetsch & Blaxter 2017. BlobTools: Interrogation of genome assemblies [version 1; referees: awaiting peer review]. F1000Research, 6:1287 (doi: 10.12688/f1000research.12232.1)
We will be presenting a poster describing BlobToolKit at Genome Science 2018 For more details, either browse this site or take a look at the project code on GitHub.
Visualise assemblies using the new BlobToolKit viewer (blobtoolkit.genomehubs.org/view/, github.com/blobtoolkit/viewer): Example using data obtained from ENA for the Pacific oyster Crassostrea gigas (AFTI01). Processed using a BlobToolKit Snakemake pipeline available at github.com/blobtoolkit/insdc-pipeline.
Dom Laetsch and Mark Blaxter’s BlobTools manuscript1 is now available on F1000 Research. This Manuscript describes BlobTools version 1, which is available at github.com/DRL/blobtools. 1 Laetsch & Blaxter 2017. BlobTools: Interrogation of genome assemblies [version 1; referees: awaiting peer review]. F1000Research, 6:1287 (doi: 10.12688/f1000research.12232.1)