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.
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
from sequana import KrakenResults, sequana_data test_file = sequana_data("test_kraken.out", "testing") k = KrakenResults(test_file) df = k.plot(kind='pie') print(df)
others 1.534356 Measles virus strain Edmonston-Zagreb 5.737158 Measles virus strain MVi/California.USA/8.04 6.337558 Measles virus genotypes and isolates 6.871247 Unclassified 12.274850 Measles virus 67.244830 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:
from sequana import KrakenResults, sequana_data test_file = sequana_data("test_kraken.out", "testing") k = KrakenResults(test_file) k.to_js(onweb=False) # The output filame is krona.html by default
ktImportText /home/docs/checkouts/readthedocs.org/user_builds/sequana/conda/master/lib/python3.5/site-packages/sequana-0.5.2-py3.5.egg/sequana/resources/testing/test_kraken.out.summary -o krona.html tput: No value for $TERM and no -T specified Writing krona.html...
An example is available in Krona example
Total running time of the script: (0 minutes 0.620 seconds)