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

Parasites & Vectors

Table 1 MinION sequencing run metadata, Albacore [18] basecalling results for both 1D and 1Dsq basecalling and read statistics

Name used in this document	AWB_0150	AWB_0157	AWB_2331	AWB_2338	Beaver_2302	Beaver_2309	BGS_2237	BGS_2244
Run name	SRRun1	SRRun1	SRRun2	SRRun2	SRRun3	SRRun3	SRRun4	SRRun4
Run ID	20170720_0150_GiardiaWB_20170719	20170720_0157_GiardiaWB_20170719	20170721_2331_GiardiaWB_20170721	20170721_2338_GiardiaWB_20170721	20170726_2302_GiardiaBeaver_20170726	20170726_2309_GiardiaBeaver_20170726	20170731_2237_GiardiaGS_20170731	20170731_2244_GiardiaGS_20170731
Isolate	Giardia AWB	Giardia AWB	Giardia AWB	Giardia AWB	Giardia beaver	Giardia beaver	Giardia BGS	Giardia BGS
Reference genome size (bp)	12,827,416	12,827,416	12,827,416	12,827,416	na	na	11,001,532	11,001,532
Sequencing depth (X genome size)	0.5	184.6	0.1	9.9	0.7	246.8	0.9	757.6
Total no. of 1D reads	1225	329,039	237	19,531	1668	382,740	1508	885,046
No. of 1D reads pass	1207	304,219	152	15,842	1603	354,581	1449	804,942
No. of 1D reads fail	18	24,820	85	3689	65	28,159	59	80,104
Percent of 1D reads passing	98.5	92.5	64.1	81.1	96.1	92.6	96.1	90.9
Total no. of IDsq reads	172	60,156	16	1904	146	53,553	212	143,371
No. of 1Dsq reads pass	68	25,755	0	192	69	29,349	124	62,452
No. of 1Dsq reads fail	104	34,401	16	1712	77	24,204	88	80,919
Average length of 1D reads	5066.15	7195.29	3450.08	6484.00	5113.00	8270.88	6534.03	9417.60
Longest 1D read	42,781	470,735	32,138	330,795	37,229	1,132,445	56,642	485,807
Average length of 1Dsq reads	5335.22	7685.61	2853.62	7344.74	5273.86	8472.84	5529.57	9829.82
Longest 1Dsq read	18,489	43,102	6523	32,705	22,740	59,564	25,876	66,185

Notes: “Pass” and “fail” refer to reads that met or did not meet the quality threshold, respectively. Run 2 was conducted on a previously used flow cell after 64–72 h run time and so had few pores left
Abbreviations: na, not applicable

ISSN: 1756-3305