Category Archives: k-mer

Extensive but not comprehensive compilation of de-novo assemblers

This figure is an update of Figure 1 in “A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.” published by Zhang et al (2011).
The figure was produced in SVG so you should be able to click on the name of the assembler which should take you straight to the PUBMED abstract. The size of the de-novo assembler names is relative to the number of citations in PUBMED. You can see that 2012 was the year of the De Brujin Graph assemblers.

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Update Kraken databases

Kraken is a really good k-mer based classification tool. I frequently use this tool for viral signal detection in metagenomic samples. A number of useful scripts such as updating Kraken databases are provided with the tool. Since the NCBI updated the FTP website structure and decided to phase-out Genbank Idenfiers (GIs), the default Kraken database update scripts do not work. So I decided to write a little python script to update Kraken databases that some Kraken users might find useful.

This script automatically downloads:

  • Human genome – most recent assembly version
  • Complete bacterial reference genomes
  • Complete viral reference genomes
  • Archaeal genomes
  • Reference plasmids sequences

This script takes an optional command-line argument which can be specified as the target location where the data should be downloaded and saved. By default, all files are downloaded in the present working directory.

To change default genome downloads e.g. download mouse reference genome instead of human; please make necessary changes in the code. Feel free to fork this script on github.

Bioinformatician at CVR.
http://bioinformatics.cvr.ac.uk/sejal.php