I am trying to do comparison between the assembly of different Streptococcus pneumoniae strains and my S. pneumoniae strain. I downloaded several complete genomes from the NCBI using datasets. Then I downloaded taxonomy and added each genome to library using --add-to-library. However, when I inspect the database using kraken2-inspect I get very low representation of the downloaded genomes. Below the database inspection. I think that this is because its mapping all the assemblies to the higher taxon (1313).
How can I correct this in order to have kmer collection for all the assemblies? Thanks!
Hello!
I am trying to do comparison between the assembly of different Streptococcus pneumoniae strains and my S. pneumoniae strain. I downloaded several complete genomes from the NCBI using
datasets. Then I downloaded taxonomy and added each genome to library using--add-to-library. However, when I inspect the database usingkraken2-inspectI get very low representation of the downloaded genomes. Below the database inspection. I think that this is because its mapping all the assemblies to the higher taxon (1313).How can I correct this in order to have kmer collection for all the assemblies? Thanks!
100.00 3559482 0 G 1301 Streptococcus 100.00 3559482 3438745 S 1313 Streptococcus pneumoniae 1.13 40261 40261 S1 373153 Streptococcus pneumoniae D39 0.59 21127 21127 S1 869309 Streptococcus pneumoniae SPNA45 0.41 14441 14441 S1 574093 Streptococcus pneumoniae AP200 0.28 10013 10013 S1 487214 Streptococcus pneumoniae Hungary19A-6 0.17 5878 5878 S1 1130804 Streptococcus pneumoniae ST556 0.15 5230 5230 S1 869216 Streptococcus pneumoniae INV200 0.15 5171 5171 S1 488222 Streptococcus pneumoniae JJA 0.13 4610 4610 S1 516950 Streptococcus pneumoniae CGSP14 0.06 1963 1963 S1 697283 Streptococcus pneumoniae gamPNI0373 0.05 1940 1940 S1 512566 Streptococcus pneumoniae G54 0.05 1847 1847 S1 488221 Streptococcus pneumoniae 70585 0.04 1600 1600 S1 189423 Streptococcus pneumoniae 670-6B 0.03 1118 1118 S1 1159083 Streptococcus pneumoniae PCS8235 0.02 829 829 S1 869303 Streptococcus pneumoniae SPN034156 0.02 816 816 S1 869312 Streptococcus pneumoniae SPN033038 0.02 668 668 S1 869304 Streptococcus pneumoniae SPN034183 0.02 663 663 S1 869311 Streptococcus pneumoniae SPN032672 0.02 636 636 S1 170187 Streptococcus pneumoniae TIGR4 0.01 412 412 S1 525381 Streptococcus pneumoniae TCH8431/19A 0.01 345 345 S1 869215 Streptococcus pneumoniae OXC141 0.01 336 336 S1 869269 Streptococcus pneumoniae INV104 0.01 235 235 S1 487213 Streptococcus pneumoniae Taiwan19F-14 0.01 215 215 S1 1408179 Streptococcus pneumoniae A026 0.00 145 145 S1 488223 Streptococcus pneumoniae P1031 0.00 141 141 S1 171101 Streptococcus pneumoniae R6 0.00 71 71 S1 869307 Streptococcus pneumoniae SPN994039 0.00 26 26 S1 869306 Streptococcus pneumoniae SPN994038