Pipelines to do MinION sequencing of Zika virus

Notes on libraries

Library 1

2D native barcoded library that was sequenced down on St. Croix, USVI. There were XX raw reads, of which XX were basecalled, or XX% basecalled.

Read counts after Metrichor basecalling

  • barcode01: 24415
  • barcode02: 21219
  • barcode03: 8897
  • barcode04: 31576
  • barcode05: 33059
  • barcode06: 215
  • barcode07: 19349
  • barcode08: 16519
  • barcode09: 12041
  • barcode10: 18536
  • barcode11: 25150
  • barcode12: 100
  • fail: 419911

This is 211076 classified out of 630987 total or 33% classified.

Read counts after Albacore basecalling

  • barcode01: 440
  • barcode02: 399
  • barcode03: 183
  • barcode04: 491
  • barcode05: 578
  • barcode06: 17
  • barcode07: 434
  • barcode08: 387
  • barcode09: 268
  • barcode10: 392
  • barcode11: 600
  • barcode12: 4
  • unclassified: 606755

This is 4193 classified out of 610948 total or 0.7% classified.

Library 2

Illumina library sequenced on MiSeq.

Library 3

2D native barcoded library. Basecalled and demultiplexed on Metrichor. There were 204912 raw reads, of which 203953 were basecalled by Metrichor, or 99.5% basecalled. Albacore basecalled 191802 or 94% of the raw reads.

Read counts after Metrichor basecalling

  • barcode01: 7270
  • barcode02: 2956
  • barcode03: 4864
  • barcode04: 2233
  • barcode05: 30667
  • barcode06: 36
  • barcode07: 6537
  • barcode08: 38
  • barcode09: 6426
  • barcode10: 2924
  • barcode11: 24037
  • barcode12: 63
  • fail: 115902

This is 88051 classified out of 203953 total or 43% classified.

Read counts after Albacore basecalling

  • barcode01: 208
  • barcode02: 109
  • barcode03: 234
  • barcode04: 143
  • barcode05: 362
  • barcode06: 3
  • barcode07: 245
  • barcode08: 8
  • barcode09: 290
  • barcode10: 96
  • barcode11: 393
  • barcode12: 4
  • unclassified: 187631

This is 2095 classified out of 191802 total or 1% classified.

Library 4

2D native barcoded library. Basecalled on Metrichor but not demultiplexed. Also basecalled and demultiplexed on Albacore. There were raw reads, of which XX were basecalled, or XX% basecalled.

Read counts after Albacore basecalling

  • barcode01: 565
  • barcode02: 358
  • barcode03: 381
  • barcode04: 568
  • barcode05: 977
  • barcode06: 9
  • barcode07: 283
  • barcode08: 424
  • barcode09: 425
  • barcode10: 718
  • barcode11: 640
  • barcode12: 21
  • unclassified: 43088

This is 5369 classified out of 48457 total or 11% classified.

Library 5

2D native barcoded library. Basecalled on Metrichor but not demultiplexed. Also basecalled and demultiplexed on Albacore. There were 758796 raw reads, of which 1495306 were basecalled. This looks suspiciously like the raw reads were basecalled twice, and all wrote to the same basecalled reads directory. We need to look into this in the pipeline and see what happened.

Read counts after Albacore basecalling

  • barcode01: 810
  • barcode02: 841
  • barcode03: 476
  • barcode04: 1177
  • barcode05: 1240
  • barcode06: 29
  • barcode07: 493
  • barcode08: 1833
  • barcode09: 1245
  • barcode10: 1735
  • barcode11: 473
  • barcode12: 22
  • unclassified: 1484932

This is 10374 classified out of 1495306 total or 0.7% classified.

Library 6

2D native barcoded library. Basecalled on Metrichor but not demultiplexed. Also basecalled and demultiplexed on Albacore.

Read counts after Albacore basecalling

  • barcode01: 147
  • barcode02: 259
  • barcode03: 130
  • barcode04: 217
  • barcode05: 53
  • barcode06: 3
  • barcode07: 141
  • barcode08: 239
  • barcode09: 210
  • barcode10: 254
  • barcode11: 411
  • barcode12: 3
  • unclassified: 509421

This is 2067 classified out of 511488 total or 0.4% classified.

Library 7

1D native barcoded library. Barcode kit provided by ONT was missing barcode 10. Both pools of negative control are barcoded by barcode06. No barcode10 was prepared (any reads classified as barcode10 are wrongly assigned).

Read counts after Albacore basecalling

  • barcode01: 325651
  • barcode02: 334437
  • barcode03: 344680
  • barcode04: 351069
  • barcode05: 422758
  • barcode06: 2934
  • barcode07: 281634
  • barcode08: 277140
  • barcode09: 358521
  • barcode10: 14
  • barcode11: 359125
  • barcode12: 360467
  • unclassified: 1762939

This is 3418430 classified out of 5181369 total or 66% classified.

Library 8

1D native barcoded library.

Read counts after Albacore basecalling

  • barcode01: 252124
  • barcode02: 262666
  • barcode03: 235882
  • barcode04: 216688
  • barcode05: 344248
  • barcode06: 2258
  • barcode07: 168794
  • barcode08: 102837
  • barcode09: 234858
  • barcode10: 183873
  • barcode11: 257642
  • barcode12: 1465
  • unclassified: 649461

This is 2263335 classified out of 2914252 total or 78% classified.