Identification of individual root-knot nematodes using low coverage long-read sequencing
Fig 2
Taxonomic assignment success of M. incognita reads varied by quality control and classification parameters.
Shown are NanoFilt minimum average read quality scores (y axis) against Kraken 2 confidence and minimum base quality parameter combinations (x axis). Only basecalled reads with a minimum average base quality of 7 were used. Kraken 2 “Confidence” indicates the minimum proportion of k-mers required for taxonomic assignment. Kraken 2 “Minimum base quality” indicates the base quality threshold at which k-mer bases are not considered ambiguous during assignment. Sections show taxonomic assignment of reads (n) to the genus Meloidogyne and lower taxonomic levels for each configuration of parameters. Each configuration is applied to the same M. incognita sample. For each chart the distance from the inner circle represents NCBI taxonomic lineage length; the inner segment is genus level assignment, the second segments are species level assignments (including the MIG species group). MIG species populate the outermost segments, internal to the MIG species group assignments. Segment widths denote proportion reads assigned to that taxonomic level or species.