Assessment of the Drosophila melanogaster ISO1 ref. strain genome (69X NanoPore data) assemblies using NextDenovo, Canu, Flye, Shasta and Wtdbg¶

Download reads

SRA Accession: SRR6702603, SRR6821890

Prepare input file (input.fofn)

ls SRR6702603.fasta.gz SRR6821890.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 = ont # clr, ont, hifi
input_fofn = input.fofn
workdir = 01_rundir

[correct_option]
read_cutoff = 1k
genome_size = 130m # estimated genome size
sort_options = -m 30g -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             25701192                   1
N20             22251987                   2
N30             22251987                   2
N40             21195733                   3
N50             21195733                   3
N60             18110856                   4
N70             13648743                   5
N80              6408543                   6
N90              1033518                  12

Min.               18454                   -
Max.            25701192                   -
Ave.             1826448                   -
Total          133330776                  73

Assemble with shasta

shasta-Linux-0.5.1  --input SRR6702603.fasta --input SRR6821890.fasta --threads 30

Download reference

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz
gzip -d GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz

Run Quast v5.0.2

quast.py --large --eukaryote --min-identity 80 --threads 30 -r GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna nextDenovo.asm.fa Canu.asm.fa Flye.asm.fa Shasta.asm.fa Wtdbg.asm.fa
Quast result

NextDenovo Canu Flye Shasta Wtdbg

# contigs 73 424 461 872 510

Largest contig 25701192 14715425 12613153 1801407 23221757

Total length 133330776 140540470 135880693 129225244 132926651

N50 21195733 4298595 6016667 535885 12028162

NG50 18110856 4298595 6016667 440773 10631323

N75 13648743 777595 2182645 244480 3308195

NG75 3925274 714013 1367004 182722 1752322

LG50 4 11 9 92 5

LG75 7 36 20 218 13

# misassemblies 345 971 724 262 616

# misassembled contigs 48 226 217 78 191

# local misassemblies 137 433 670 123 185

# unaligned mis. contigs 1 3 5 7 36

# unaligned contigs 1 + 36 part 8 + 122 part 11 + 118 part 191 + 76 part 89 + 291 part

Unaligned length 603053 769264 811595 1660668 2264882

Genome fraction (%) 92.109 93.614 91.799 88.085 91.504

Duplication ratio 1.011 1.047 1.032 1.016 1.002

# mismatches per 100 kbp 90.86 183.12 220.48 609.69 179.86

# indels per 100 kbp 567.78 831.54 1334.52 1428.10 1081.15

Largest alignment 25696021 11699048 11981267 1799773 18844039

Total aligned length 132416893 139189216 134650393 127438699 130313270

NA50 6618721 3863099 5596752 527231 4309906

NGA50 6618721 3863099 5143715 434179 4174617

NA75 3269191 670044 1955654 230034 1573933

NGA75 2125978 611559 1267543 168924 928918

LGA50 5 13 11 94 10

LGA75 14 42 24 227 27

Note

The results of Canu, Flye and Wtdbg are copied from ftp://ftp.dfci.harvard.edu/pub/hli/wtdbg/dm-ISO1, published by wtdbg2 paper, the complete result of Quast can be seen from here.