BlobToolKit https://blobtoolkit.genomehubs.org Wed, 26 Jun 2019 08:06:12 +0000 en-US hourly 1 https://wordpress.org/?v=6.4.8 https://blobtoolkit.genomehubs.org/wp-content/uploads/2019/08/cropped-hex_logo-32x32.png BlobToolKit https://blobtoolkit.genomehubs.org 32 32 Introducing BlobToolKit https://blobtoolkit.genomehubs.org/2019/02/11/introducing-blobtoolkit-2/ Mon, 11 Feb 2019 14:30:57 +0000 https://blobtoolkit.genomehubs.org/?p=148 BlobToolKit is a set of tools to allow interactive exploration, assessment and filtering of genomic datasets. The main tools are BlobTools2, a re-implementation of BobTools to support additional features and The BlobToolKit Viewer, which allows interactive exploration of datasets.

This series of blog posts aims to introduce many of the features in BlobToolKit and provide a set of examples to help you get started with your own data.  Further documentation is available on the BlobToolKit GitHub pages: BlobTools2 and BlobToolKit Viewer.

  1. Getting Started with BlobTools2
  2. Interactive blobology (coming soon)

Example plots generated by the BlobToolKit Viewer:

]]> Genome Science 2018 https://blobtoolkit.genomehubs.org/2018/08/30/genome-science-2018/ Thu, 30 Aug 2018 14:10:12 +0000 https://blobtoolkit.genomehubs.org/?p=130 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.

]]> BlobToolKit Viewer https://blobtoolkit.genomehubs.org/2018/07/13/blobtoolkit-viewer/ Fri, 13 Jul 2018 12:30:01 +0000 https://blobtoolkit.genomehubs.org/?p=91 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.
]]> BlobTools manuscript now available https://blobtoolkit.genomehubs.org/2017/08/01/blobtools-manuscript-now-available/ Tue, 01 Aug 2017 15:34:31 +0000 http://wordpress.genomehubs.org/?p=66 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)

]]> Introducing BlobToolKit https://blobtoolkit.genomehubs.org/2017/06/28/introducing-blobtoolkit/ Wed, 28 Jun 2017 15:33:10 +0000 http://wordpress.genomehubs.org/?p=64 The BlobToolKit project has been funded by the BBSRC for 3 years to develop the latest iteration of the Blobology/Blobtools genome assembly QC, visualisation and filtering tools. The project is a collaboration between the research groups of Mark Blaxter at the University of Edinburgh and Guy Cochrane at EMBL-EBI to develop software tools and protocols to aid in the separation of cobionts and removal of contaminants from genomic datasets prior to genome sequence assembly.

BlobToolKit follows on from the development of Blobology1 and BlobTools2 over the past few years in the Blaxter Lab at the University of Edinburgh. As development on BlobToolKit has only just begun, users interested in applying these approaches should continue to use Dom Laetsch’s BlobTools package directly until the methods are fully incorporated into BlobToolKit.

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 GitHub – DRL/blobtools: Application for the visualisation of draft genome assemblies and general QC (available at https://github.com/DRL/blobtools).

Update [2017-08-01]:
The BlobTools Manuscript is now available on F1000 research
Laetsch & Blaxter 2017. BlobTools: Interrogation of genome assemblies [version 1; referees: awaiting peer review]. F1000Research, 6:1287 (doi: 10.12688/f1000research.12232.1)

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