5.5. Kraken module example
In Sequana, we provide tools to quickly assess the taxonomic content of a reads (FastQ). It is based on the Kraken and Krona software. Sequana bridges the gap between those tools, Kraken databases and a simple interface to get a quick taxonomic overview of the FastQ content.
For more information, please see the
sequana.kraken module documentation.
Note that this feature is also part of the quality_control pipeline.
Although we will use the Sequana library hereafter, note that there is also a standalone application named sequana_taxonomy.
C HISEQ:426:C5T65ACXX:5:2301:5633:7203 11234 203 0:2 11234:1 0:1 11234:1 0:2 11234:1 0:13 11234:1 0:1 11234:1 0:3 11234:1 0:16 11234:1 0:5 11234:1 0:6 11234:1 0:13 A:31 0:33 11234:1 0:29 11234:1 0:7 C HISEQ:426:C5T65ACXX:5:2301:5815:7120 11234 203 0:4 11234:1 0:12 11234:1 0:22 11234:1 0:1 0 11234:1 0:5 11234:1 0:7 11234:1 0:5 A:31 0:3 11234:1 0:22 11234:1 0:18 11234:1 0:24 11234:1
Each row correspond to a read in the FastQ file(s). The first column is either C (classified) or U (unclassified) and the third column contains the taxon the most relevant.
The taxon are not readable so we first need to get the scientific names
Besides, the lineage would be useful. This is done in Sequana using
sequana.kraken.KrakenResults. See following example.
In the following example, we use the results of a kraken analysis. The original toy data files contains 1500 reads mostly related to Measles virus
name:Measles virus genotype G3 1.010101 name:Measles virus genotypes and isolates 3.030303 name:Measles virus strain MVi/California.USA/8.04 8.080808 name:Measles virus strain Edmonston-Zagreb 8.080808 Unclassified 10.101010 name:Measles virus 69.696970 dtype: float64
Note that only a subset of taxons are shown in the pie chart that is those that cover at least 1% of the total reads. Others are put together and labelled "others"
A more interactive plot can be obtained using Krona if installed:
An example is available in Krona example
Total running time of the script: (0 minutes 0.119 seconds)