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¶

Download reads

SRA Accession: SRX1715706, SRX1715705, SRX1715704, SRX1715703

Prepare input file (input.fofn)

ls f1.fasta.gz > input.fofn

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

Run

nohup nextDenovo run.cfg &

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

Assemble with shasta

shasta-Linux-0.5.1 --input f1.fasta --threads 30

Download reference

wget ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas

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.