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Table 2 Genome assembly statistics and summary

From: Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei

Genome

Step

Software

Sizea

# contigsb

# scaffolds

Average lengthc

N50d

N90e

Tcm

454 assembly

CELERA

37.3

30,737

-

1,216

1,670

539

Illumina assembly

Velvet (kmer 43)

16.7

9,247

-

1,813

2,378

851

Assembly of non-assembled Illumina reads

Velvet (kmer 53)

1.17

2,094

-

562

536

418

Assembly merging

Zorro

33.5

24,799 f

-

1,353

2,218

549

Scaffolding

SSPACE

38.8

23,813 f

1,835

2,296

25,044

576

Gap closure

IMAGE

38.6

23,000

1,774

2,302

25,781

583

Tcc X10

454 assembly

CELERA

41.8

33,686

-

1,243

1,516

549

Illumina assembly

Velvet (kmer 43)

17.0

8,523

-

1,997

2,742

904

Assembly of non-assembled Illumina reads

Velvet (kmer 53)

1.14

2,116

-

543

523

416

Assembly merging

Zorro

38.0

28,389 f

-

1,339

1,869

560

Scaffolding

SSPACE

43.7

27,605 f

2,476

2,162

14,067

589

Gap closure

IMAGE

43.4

26,889

2,423

2,158

14,516

592

  1. a The length when sequences are combined (Mb).
  2. b The number of contigs/scaffolds.
  3. c The average contig length (bp). For the SSPACE row, this refers to the average scaffold length.
  4. d The length N for which half of all bases are in a sequence of this length or longer.
  5. e The length N for which 90% of all bases are in a sequence of this length or longer.
  6. f Contigs >500 bp.