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Table 2 Sequencing datasets and genome mapping of the Daphnia pulex TCO library.

From: SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data

Reads collection

Sequencing runs/collection

Library fraction

Raw reads

Cleaned reads

Mapped reads

Mapped/Cleaned reads (%)

Run time (min)

Added run (multiplex, read length)

LF1

LF1

Large only

383,575

381,612

311,919

81.74

7.1

LF1 (36 ×, 2 × 151)

LF1-2

LF1+LF2

Large only

1,083,738

1,076,671

907,601

84.30

13.8

LF2 (36 ×, 2 × 251)

LF1-3

LF1+LF2+LF3

Large only

1,782,006

1,743,523

1,478,140

84.78

21.7

LF3 (36 ×, 2 × 251)

LF1-4

LF1+LF2+LF3+LF4

Large only

2,218,000

2,177,265

1,848,979

84.92

26.1

LF4 (36 ×, 2 × 251)

LF1-5

LF1+LF2+LF3+LF4+LF5

Large only

4,242,048

4,178,856

3,524,528

84.34

45.9

LF5 (6 ×, 2 × 251)

LF1-5SF1

LF1+LF2+LF3+LF4+LF5+SF1

Large + Small

4,542,917

4,478,675

3,766,787

84.10

48.1

SF1 (36 ×, 2 × 151)

LF1-5 SF1-2

LF1+LF2+LF3+LF4+LF5+SF1+SF2

Large + Small

5,084,493

5,014,933

4,204,692

83.84

50.6

SF2 (36 ×, 2 × 151)

LF1-5 SF1-3

LF1+LF2+LF3+LF4+LF5+SF1+SF2+SF3

Large + Small

5,530,560

5,457,878

4,561,648

83.58

52.7

SF3 (36 ×, 2 × 151)

LF1-5 SF1-4

LF1+LF2+LF3+LF4+LF5+SF1+SF2+SF3+SF4

Large + Small

5,920,185

5,845,827

4,872,885

83.36

54.8

SF4 (36 ×, 2 × 151)

LF1-5 SF1-5

LF1+LF2+LF3+LF4+LF5+SF1+SF2+SF3+SF4+SF5

Large + Small

6,411,123

6,333,054

5,270,616

83.22

56.5

SF5 (36 ×, 2 × 151)

  1. All the NGS run datasets were generated by sequencing the TCO gDNA library which was split into two fractions: a large fraction (LF) with an average insert size of 572 bp and a small fraction (SF) with an average insert size of 269 bp. An Illumina MiSeq was used for sequencing and both fractions were each sequenced five times in a 36 × or 6 × multiplexing fashion, resulting in datasets LF1 to LF5 and SF1 to SF5. The reads collections were mapped to a D. pulex reference genome by running the SA_Run2Ref workflow.