Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation

Parasites & Vectors

Table 2 Read error profiles for Giardia AWB and Giardia BGS MinION sequencing runs

Error type/reads	AWB_0150	AWB_0157	AWB_2331	AWB_2338	BGS_2237	BGS_2244
Proportion of reads counted (%)	87.55	83.56	28.04	52.61	12.62	77.47
Overall base identity (%)	76.907	74.577	54.293	65.904	58.255	56.636
Overall base identity error rate (%)	23.093	25.423	45.707	34.096	41.745	43.364
Aligned base identity (%)	90.526	89.352	83.076	83.915	91.429	89.954
Aligned base identity error rate (%)	9.474	10.648	16.924	16.085	8.571	10.046
Identical bases per 100	80.430	78.338	71.024	71.597	80.855	78.834
Inserted bases per 100	5.291	3.881	7.811	5.087	3.473	4.478
Deleted bases per 100	5.860	8.450	6.758	9.592	8.105	7.886
Substitutions per 100	8.415	9.334	14.406	13.725	7.569	8.801
Mean insertion	1.638	1.462	1.755	1.480	1.482	1.530
Mean deletion	1.621	1.787	1.591	1.788	1.848	1.898

Notes: Using NanoOK [26], 1D reads were aligned to the corresponding reference genome and the error profiles of aligned reads were evaluated. NanoOK outputs read error profiles for each reference contig. To obtain overall error profiles for all reads, the values for each contig were multiplied by the proportion of total reads that aligned to that contig. The sum of these values for each error metric were scaled according to the proportion of total sequencing reads that were used for NanoOK’s analysis

ISSN: 1756-3305