Assembly Report
11 April, 2025
Global Asm4pg assembly report for: QRobur_dtol_hic
Asm4pg Parameters
Hifiasm mode : hi-c
If hi-c or trio mode :
- parent1/r1 clean_R1.fastq.gz
- parent2/r2 clean_R2.fastq.gz
Hifiasm purge force : 3
Purge_dups executed: No
Genome scafolded: No
Busco lineage: eudicots_odb10
Genome ploidy: 2
Kmers size: 21
Raw data QC
Reads statistics
# number of contigs: 4566215
# total contigs length: 63260161666
# mean contig size: 13853.96
# contig size first quartile: 9294
# median contig size: 13919
# contig size third quartile: 17865
# longest contig: 53004
# shortest contig: 51
# contigs > 500 nt: 4563690 (99.94 %)
# contigs > 1K nt: 4562727 (99.92 %)
# contigs > 10K nt: 3282316 (71.88 %)
# contigs > 100K nt: 0 (0.00 %)
# contigs > 1M nt: 0 (0.00 %)
# N50: 16322
# L50: 1553029
# N80: 11702
# L80: 2901515QC on final assembly
Assembly statistics
Hap 1
# number of contigs: 877
# total contigs length: 849314776
# mean contig size: 968431.90
# contig size first quartile: 35721
# median contig size: 45222
# contig size third quartile: 70000
# longest contig: 98921506
# shortest contig: 1000
# contigs > 500 nt: 877 (100.00 %)
# contigs > 1K nt: 871 (99.32 %)
# contigs > 10K nt: 863 (98.40 %)
# contigs > 100K nt: 96 (10.95 %)
# contigs > 1M nt: 13 (1.48 %)
# N50: 62438176
# L50: 6
# N80: 54344288
# L80: 10Hap 2
# number of contigs: 112
# total contigs length: 809654976
# mean contig size: 7229062.29
# contig size first quartile: 34102
# median contig size: 50665
# contig size third quartile: 139789
# longest contig: 100233192
# shortest contig: 1000
# contigs > 500 nt: 112 (100.00 %)
# contigs > 1K nt: 111 (99.11 %)
# contigs > 10K nt: 107 (95.54 %)
# contigs > 100K nt: 33 (29.46 %)
# contigs > 1M nt: 14 (12.50 %)
# N50: 67606007
# L50: 5
# N80: 55358563
# L80: 10K-mer profiles
| Hap 1 | Hap 2 |
|---|---|
 |
 |
K-mer completeness and error rate
Completeness
tmp_hap2 all 482294416 623596779 77.3407Error rate
tmp_hap2 7439 809633296 63.5899 4.37531e-07BUSCO score
Hap 1
# BUSCO version is: 5.7.1
# The lineage dataset is: eudicots_odb10 (Creation date: 2024-01-08, number of genomes: 31, number of BUSCOs: 2326)
# Summarized benchmarking in BUSCO notation for file /home/lpiat/work/asm_article_benchmark/asm_hic/results/asm4pg_hic_results/02_final_assembly/hap1/asm4pg_hic_final_hap1.fasta
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot
***** Results: *****
C:98.4%[S:93.7%,D:4.7%],F:1.1%,M:0.5%,n:2326,E:2.6%
2290 Complete BUSCOs (C) (of which 60 contain internal stop codons)
2180 Complete and single-copy BUSCOs (S)
110 Complete and duplicated BUSCOs (D)
25 Fragmented BUSCOs (F)
11 Missing BUSCOs (M)
2326 Total BUSCO groups searched
Assembly Statistics:
877 Number of scaffolds
1086 Number of contigs
849314776 Total length
0.002% Percent gaps
62 MB Scaffold N50
42 MB Contigs N50
Dependencies and versions:
hmmsearch: 3.1
bbtools: 39.01
miniprot_index: 0.13-r248
miniprot_align: 0.13-r248
python: sys.version_info(major=3, minor=7, micro=12, releaselevel='final', serial=0)
busco: 5.7.1Hap 2
# BUSCO version is: 5.7.1
# The lineage dataset is: eudicots_odb10 (Creation date: 2024-01-08, number of genomes: 31, number of BUSCOs: 2326)
# Summarized benchmarking in BUSCO notation for file /home/lpiat/work/asm_article_benchmark/asm_hic/results/asm4pg_hic_results/02_final_assembly/hap2/asm4pg_hic_final_hap2.fasta
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot
***** Results: *****
C:98.6%[S:93.9%,D:4.7%],F:0.9%,M:0.5%,n:2326,E:2.4%
2294 Complete BUSCOs (C) (of which 56 contain internal stop codons)
2184 Complete and single-copy BUSCOs (S)
110 Complete and duplicated BUSCOs (D)
21 Fragmented BUSCOs (F)
11 Missing BUSCOs (M)
2326 Total BUSCO groups searched
Assembly Statistics:
112 Number of scaffolds
274 Number of contigs
809654976 Total length
0.002% Percent gaps
67 MB Scaffold N50
39 MB Contigs N50
Dependencies and versions:
hmmsearch: 3.1
bbtools: 39.01
miniprot_index: 0.13-r248
miniprot_align: 0.13-r248
python: sys.version_info(major=3, minor=7, micro=12, releaselevel='final', serial=0)
busco: 5.7.1Telomeres
Telomeres present in assembly #### Hap 1
##########
877 sequences to analyze for telomeric repeats (TTAGGG/CCCTAA) in file /home/lpiat/work/asm_article_benchmark/asm_hic/results/asm4pg_hic_results/02_final_assembly/hap1/asm4pg_hic_final_hap1.fasta
##########
scaffold_1 Forward (start of sequence) AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
scaffold_1 Reverse (end of sequence) GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
scaffold_2 Forward (start of sequence) CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC
scaffold_2 Reverse (end of sequence) GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
scaffold_3 Forward (start of sequence) CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC
scaffold_3 Reverse (end of sequence) AGGGTTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTT
scaffold_4 Forward (start of sequence) CCTAAACCCTAAACCCTATAACCCTAAACCCTAAACCCTAAACCCTAAAC
scaffold_4 Reverse (end of sequence) TTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTT
scaffold_5 Reverse (end of sequence) GGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGG
scaffold_6 Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
scaffold_7 Forward (start of sequence) TAAACCCCTAAACCCTATTAAAGCCCTAAACCCTACCCAAAACCTAAACC
scaffold_7 Reverse (end of sequence) TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTT
scaffold_8 Forward (start of sequence) CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
scaffold_9 Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
scaffold_9 Reverse (end of sequence) GGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAG
scaffold_10 Forward (start of sequence) CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC
scaffold_10 Reverse (end of sequence) TTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTT
scaffold_11 Forward (start of sequence) AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
scaffold_11 Reverse (end of sequence) TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTT
scaffold_12 Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
scaffold_12 Reverse (end of sequence) GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
scaffold_14 Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAAACCCT
scaffold_19 Reverse (end of sequence) GTTTAGGGTTTAGGGTTTAGGGGTTTAGGGTTAGGGTTTAGTAGGGTTGT
Telomeres found: 23 (12 forward, 11 reverse)Hap 2
##########
112 sequences to analyze for telomeric repeats (TTAGGG/CCCTAA) in file /home/lpiat/work/asm_article_benchmark/asm_hic/results/asm4pg_hic_results/02_final_assembly/hap2/asm4pg_hic_final_hap2.fasta
##########
scaffold_1 Forward (start of sequence) ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
scaffold_1 Reverse (end of sequence) TTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGT
scaffold_2 Forward (start of sequence) CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
scaffold_2 Reverse (end of sequence) TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTT
scaffold_3 Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
scaffold_3 Reverse (end of sequence) GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
scaffold_4 Reverse (end of sequence) TTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTT
scaffold_5 Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
scaffold_5 Reverse (end of sequence) GTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
scaffold_6 Forward (start of sequence) CGCTAAACCCTAAACCCTAAACCCCTAAAACCCTAAACCCTAAACCCTAC
scaffold_6 Reverse (end of sequence) TTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGT
scaffold_7 Forward (start of sequence) CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
scaffold_7 Reverse (end of sequence) GGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAG
scaffold_8 Forward (start of sequence) TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
scaffold_8 Reverse (end of sequence) GGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAG
scaffold_9 Forward (start of sequence) CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC
scaffold_9 Reverse (end of sequence) AGGGTTTAGGGTTTAGGTTTAGGGTTTAGGGTTTAGGGGTTTAGGGTTTA
scaffold_10 Forward (start of sequence) AACCACCAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
scaffold_10 Reverse (end of sequence) TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTT
scaffold_11 Forward (start of sequence) ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
scaffold_11 Reverse (end of sequence) GGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGG
scaffold_12 Forward (start of sequence) CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
scaffold_12 Reverse (end of sequence) GGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTTT
scaffold_34 Forward (start of sequence) TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
Telomeres found: 24 (12 forward, 12 reverse)Transposable element analysis
Hap 1
LTR recap
==================================================
file name: tmp_hap.fasta
sequences: 877
total length: 849314776 bp (849293876 bp excl N/X-runs)
GC level: 35.84 %
bases masked: 338617518 bp ( 39.87 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 655589 338617518 bp 39.87 %
SINEs: 0 0 bp 0.00 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 655589 338617518 bp 39.87 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 99659 48028055 bp 5.65 %
Gypsy/DIRS1 100728 94037381 bp 11.07 %
Retroviral 0 0 bp 0.00 %
DNA transposons 0 0 bp 0.00 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 0 0 bp 0.00 %
Total interspersed repeats: 338617518 bp 39.87 %
Small RNA: 0 0 bp 0.00 %
Satellites: 0 0 bp 0.00 %
Simple repeats: 0 0 bp 0.00 %
Low complexity: 0 0 bp 0.00 %
==================================================LAI
Chr From To Intact Total raw_LAI LAI
whole_genome 1 849293876 0.0671 0.3911 17.15 22.78Hap 2
LTR recap
==================================================
file name: tmp_hap.fasta
sequences: 112
total length: 809654976 bp (809638776 bp excl N/X-runs)
GC level: 35.75 %
bases masked: 304230671 bp ( 37.58 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 597925 304230671 bp 37.58 %
SINEs: 0 0 bp 0.00 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 597925 304230671 bp 37.58 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 113613 56848832 bp 7.02 %
Gypsy/DIRS1 107312 67044763 bp 8.28 %
Retroviral 0 0 bp 0.00 %
DNA transposons 0 0 bp 0.00 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 0 0 bp 0.00 %
Total interspersed repeats: 304230671 bp 37.58 %
Small RNA: 0 0 bp 0.00 %
Satellites: 0 0 bp 0.00 %
Simple repeats: 0 0 bp 0.00 %
Low complexity: 0 0 bp 0.00 %
==================================================LAI
Chr From To Intact Total raw_LAI LAI
whole_genome 1 809638776 0.0694 0.3681 18.85 23.58