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

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

Name used in this documentAWB_0150AWB_0157AWB_2331AWB_2338Beaver_2302Beaver_2309BGS_2237BGS_2244
Run nameSRRun1SRRun1SRRun2SRRun2SRRun3SRRun3SRRun4SRRun4
Run ID20170720_0150_GiardiaWB_2017071920170720_0157_GiardiaWB_2017071920170721_2331_GiardiaWB_2017072120170721_2338_GiardiaWB_2017072120170726_2302_GiardiaBeaver_2017072620170726_2309_GiardiaBeaver_2017072620170731_2237_GiardiaGS_2017073120170731_2244_GiardiaGS_20170731
IsolateGiardia AWBGiardia AWBGiardia AWBGiardia AWBGiardia beaverGiardia beaverGiardia BGSGiardia BGS
Reference genome size (bp)12,827,41612,827,41612,827,41612,827,416nana11,001,53211,001,532
Sequencing depth (X genome size)0.5184.60.19.90.7246.80.9757.6
Total no. of 1D reads1225329,03923719,5311668382,7401508885,046
No. of 1D reads pass1207304,21915215,8421603354,5811449804,942
No. of 1D reads fail1824,8208536896528,1595980,104
Percent of 1D reads passing98.592.564.181.196.192.696.190.9
Total no. of IDsq reads17260,15616190414653,553212143,371
No. of 1Dsq reads pass6825,75501926929,34912462,452
No. of 1Dsq reads fail10434,4011617127724,2048880,919
Average length of 1D reads5066.157195.293450.086484.005113.008270.886534.039417.60
Longest 1D read42,781470,73532,138330,79537,2291,132,44556,642485,807
Average length of 1Dsq reads5335.227685.612853.627344.745273.868472.845529.579829.82
Longest 1Dsq read18,48943,102652332,70522,74059,56425,87666,185
  1. 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
  2. Abbreviations: na, not applicable