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Table 3 Assembly of down-sampled Caenorhabditis elegans read sets

From: Identification and characterization of alternative splicing in parasitic nematode transcriptomes

 

Full

Random subset

Normalized subset

Assembly statistics

   

Reads used

1746642

698656

809855

Average read length

403

403

383

% aligned reads

96.70%

94.05%

92.68%

Isotigs

16772

12132

17322

Isotig N50

598

569

599

Isogroups

15940

11746

16129

AS Isogroups

708 (2.65%)

341 (2.90%)

1026 (6.36%)

Average isotigs per AS isogroup

2.20

2.13

2.16

Accuracy

   

Fragmentation

9.90%

6.30%

9.60%

BLASTN v. CDSs

   

Isotigs with match1

6385 (38.07%)

4424 (36.47%)

6422 (37.07%)

Isogroups with match2

6294 (39.49%)

4380 (37.29%)

6224 (38.59%)

C. elegans genes matched

5727 (27.92%)

4213 (20.10%)

5628 (27.43%)

  1. 1Matches were required to meet a cutoff of ≥90% nucleotide sequence identity over ≥75% of the length of the isotigs in a single high-scoring segment pair.
  2. 2Matching isogroups are defined as isogroups containing ≥1 isotig matched to a C. elegans feature.
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Parasites & Vectors

ISSN: 1756-3305

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