Assessment of the Arabidopsis thaliana F1 generation of Col-0 and Cvi-0 strains genome (~1% heterozygosity, 192X PacBio CLR reads) assemblies using NextDenovo, Canu, Falcon, Flye, Shasta, Mecat and Wtdbg

  1. Download reads

SRA Accession: SRX1715706, SRX1715705, SRX1715704, SRX1715703
  1. Prepare input file (input.fofn)

ls f1.fasta.gz > input.fofn
  1. Prepare config file (run.cfg)

[General]
job_type = sge # here we use SGE to manage jobs
job_prefix = nextDenovo
task = all
rewrite = yes
deltmp = yes
parallel_jobs = 12
input_type = raw
read_type = clr # clr, ont, hifi
input_fofn = input.fofn
workdir = 01_rundir

[correct_option]
read_cutoff = 1k
genome_size = 120m # estimated genome size
sort_options = -m 50g -t 35
minimap2_options_raw = -t 20
pa_correction = 6
correction_options = -p 35

[assemble_option]
minimap2_options_cns = -t 20
nextgraph_options = -a 1
  1. Run

nohup nextDenovo run.cfg &
  1. Get result

  • Final corrected reads file (use the -b parameter to get more corrected reads):

    01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta
    
  • Final assembly result:

    01_rundir/03.ctg_graph/nd.asm.fasta
    

    The folowing is the assembly statistics:

    Type           Length (bp)            Count (#)
    N10             13144176                   1
    N20             13090493                   2
    N30              9367478                   4
    N40              9212899                   5
    N50              8798661                   6
    N60              5544810                   8
    N70              3588034                  11
    N80              2192782                  16
    N90               688550                  25
    
    Min.               26566                   -
    Max.            13144176                   -
    Ave.             1434812                   -
    Total          126263508                  88
    
  1. Assemble with shasta

shasta-Linux-0.5.1 --input f1.fasta --threads 30
  1. Download reference

wget ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas
  1. Run Quast v5.0.2

quast.py --large --eukaryote --min-identity 80 --threads 30 -r TAIR10_chr_all.fa nextDenovo.asm.fa Canu.asm.fa Falcon.asm.fa Flye.asm.fa Shasta.asm.fa Mecat.asm.fa Wtdbg.asm.fa
Quast result

NextDenovo

Canu

Falcon

Flye

Shasta

Mecat

Wtdbg

# contigs

88

2107

171

1097

1468

1243

703

Largest contig

13144176

3980575

13319401

4836132

4378421

12631656

14128365

Total length

126263508

229056851

140024465

131553479

143148140

202215921

132890796

N50

8798661

231924

7960654

325940

357597

688687

5479602

NG50

8798661

873036

7979657

370306

560105

3525236

8707235

N75

2323231

69274

1507122

137772

93305

85155

1095469

NG75

3588034

460325

4810976

180227

185928

1096121

2182254

LG50

6

40

6

71

50

8

6

LG75

11

86

10

190

149

22

13

# misassemblies

1314

2314

1607

1570

1631

1783

1529

# misassembled contigs

63

383

89

362

357

250

156

# local misassemblies

1128

2571

1437

1189

1077

2196

1086

# unaligned mis. contigs

0

8

0

39

79

0

25

# unaligned contigs

13 + 57 part

278 + 511 part

48 + 63 part

27 + 494 part

81 + 528 part

1 + 355 part

253 + 256 part

Unaligned length

5577991

13404835

6336453

4365056

11810280

5760459

12620722

Genome fraction (%)

96.006

99.528

96.938

96.517

97.774

98.166

93.695

Duplication ratio

1.052

1.813

1.154

1.103

1.124

1.675

1.074

# mismatches per 100 kbp

668.46

1299.53

822.92

753.04

763.33

1052.95

722.82

# indels per 100 kbp

193.40

281.21

127.09

212.74

727.64

338.60

303.37

Largest alignment

5887963

3963652

10477942

4820655

3059195

5451806

7529822

Total aligned length

120235666

214635623

133317043

126764931

131090282

196116682

120017897

NA50

1136416

115341

1459104

280334

255952

202014

756810

NGA50

1504454

539509

1909294

328298

384761

901832

945708

NA75

354228

48301

270481

93990

41634

62905

192079

NGA75

472949

246039

676191

128725

118594

339389

316618

LGA50

21

60

15

82

60

27

27

LGA75

61

140

41

230

202

80

82

Note

the results of Canu, Falcon, Flye, Mecat and Wtdbg are copied from ftp://ftp.dfci.harvard.edu/pub/hli/wtdbg/at-f1, published by wtdbg2 paper, the complete result of Quast can be seen from here.