Assembly Report
14 May, 2025
Global Asm4pg assembly report for: pepper_trio
Asm4pg Parameters
Hifiasm mode : trio
If hi-c or trio mode :
- parent1/r1 sample_combined_R1.fastq.gz
- parent2/r2 sample_combined_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: 11829089
# total contigs length: 201930935177
# mean contig size: 17070.71
# contig size first quartile: 12047
# median contig size: 16879
# contig size third quartile: 21801
# longest contig: 62198
# shortest contig: 45
# contigs > 500 nt: 11828257 (99.99 %)
# contigs > 1K nt: 11827770 (99.99 %)
# contigs > 10K nt: 9780945 (82.69 %)
# contigs > 100K nt: 0 (0.00 %)
# contigs > 1M nt: 0 (0.00 %)
# N50: 19794
# L50: 4057061
# N80: 14260
# L80: 7619242QC on final assembly
Assembly statistics
Hap 1
# number of contigs: 225
# total contigs length: 3093706697
# mean contig size: 13749807.54
# contig size first quartile: 17342
# median contig size: 32746
# contig size third quartile: 131209
# longest contig: 270751445
# shortest contig: 1727
# contigs > 500 nt: 225 (100.00 %)
# contigs > 1K nt: 225 (100.00 %)
# contigs > 10K nt: 216 (96.00 %)
# contigs > 100K nt: 60 (26.67 %)
# contigs > 1M nt: 36 (16.00 %)
# N50: 189955480
# L50: 7
# N80: 122568117
# L80: 13Hap 2
# number of contigs: 313
# total contigs length: 3104393956
# mean contig size: 9918191.55
# contig size first quartile: 41870
# median contig size: 58748
# contig size third quartile: 101756
# longest contig: 263434072
# shortest contig: 14035
# contigs > 500 nt: 313 (100.00 %)
# contigs > 1K nt: 313 (100.00 %)
# contigs > 10K nt: 313 (100.00 %)
# contigs > 100K nt: 78 (24.92 %)
# contigs > 1M nt: 39 (12.46 %)
# N50: 228317904
# L50: 7
# N80: 122680256
# L80: 12K-mer profiles
| Hap 1 | Hap 2 |
|---|---|
 |
 |
K-mer completeness and error rate
Completeness
pepper_trio_hap1 all 1747538069 1862114111 93.847
pepper_trio_hap2 all 1747171574 1862114111 93.8273
both all 1849264697 1862114111 99.31
pepper_trio_hap1 pepper_trio_P1-db.hapmer 86647986 86662834 99.9829
pepper_trio_hap1 pepper_trio_P2-db.hapmer 14145 93664470 0.0151018
pepper_trio_hap2 pepper_trio_P1-db.hapmer 16519 86662834 0.0190612
pepper_trio_hap2 pepper_trio_P2-db.hapmer 91915238 93664470 98.1324
both pepper_trio_P1-db.hapmer 86648522 86662834 99.9835
both pepper_trio_P2-db.hapmer 91915638 93664470 98.1329Error rate
pepper_trio_hap1 4807 3093702197 71.3082 7.39906e-08
pepper_trio_hap2 8155 3104387696 69.0277 1.25092e-07
Both 12962 6198089893 70.018 9.95853e-08BUSCO 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_trio/results/pepper_trio_results/02_final_assembly/hap1/pepper_trio_final_hap1.fasta
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot
***** Results: *****
C:97.9%[S:94.9%,D:3.0%],F:1.6%,M:0.5%,n:2326,E:3.5%
2277 Complete BUSCOs (C) (of which 80 contain internal stop codons)
2207 Complete and single-copy BUSCOs (S)
70 Complete and duplicated BUSCOs (D)
37 Fragmented BUSCOs (F)
12 Missing BUSCOs (M)
2326 Total BUSCO groups searched
Assembly Statistics:
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_trio/results/pepper_trio_results/02_final_assembly/hap2/pepper_trio_final_hap2.fasta
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot
***** Results: *****
C:97.0%[S:94.2%,D:2.8%],F:1.6%,M:1.4%,n:2326,E:3.5%
2255 Complete BUSCOs (C) (of which 80 contain internal stop codons)
2190 Complete and single-copy BUSCOs (S)
65 Complete and duplicated BUSCOs (D)
37 Fragmented BUSCOs (F)
34 Missing BUSCOs (M)
2326 Total BUSCO groups searched
Assembly Statistics:
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
##########
225 sequences to analyze for telomeric repeats (TTAGGG/CCCTAA) in file /home/lpiat/work/asm_article_benchmark/asm_trio/results/pepper_trio_results/02_final_assembly/hap1/pepper_trio_final_hap1.fasta
##########
h1tg000002l Forward (start of sequence) TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
h1tg000005l Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTGAACCCTAAACCCTAAACCCTA
h1tg000007l Reverse (end of sequence) GGTTTAGGGTTTAGGGTTAGGGTTTAGGGATAGGGATTTCAGGGTTTAGG
h1tg000008l Reverse (end of sequence) GTTTAGGGTTTAGGTTTAGGTTTAGGGTTTAGGTTTAGGGTTTAGGGTTT
h1tg000009l Reverse (end of sequence) GGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGG
h1tg000010l Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
h1tg000016l Forward (start of sequence) AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
h1tg000019l Reverse (end of sequence) TTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGTTTAGGGTTTAGGGTTT
h1tg000020l Forward (start of sequence) CCTAAACCCTAAACCCTAACCCTAAACCCTAAACCCTAAACCCTAAACCC
h1tg000021l Forward (start of sequence) ACCCTAACCCTAAACCCTAAAACCTAAACCCTAAACCCTAAACCCTAAAC
h1tg000023l Forward (start of sequence) ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
h1tg000026l Forward (start of sequence) CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC
h1tg000032l Forward (start of sequence) CAAACCTAAACCCAATAAAACCCTAACCCTAACCCTAAACCCTAAACCCT
Telomeres found: 13 (9 forward, 4 reverse)Hap 2
##########
313 sequences to analyze for telomeric repeats (TTAGGG/CCCTAA) in file /home/lpiat/work/asm_article_benchmark/asm_trio/results/pepper_trio_results/02_final_assembly/hap2/pepper_trio_final_hap2.fasta
##########
h2tg000006l Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCTAAACCC
h2tg000008l Reverse (end of sequence) AGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTAG
h2tg000015l Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAATCCCGTAAACCCTAACCCTAAAC
h2tg000017l Forward (start of sequence) CTAAACCCTAAACCCTAACCTAACCCTAAACCCTAAACCCTAAACCCTAA
h2tg000018l Forward (start of sequence) CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
h2tg000020l Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
h2tg000027l Reverse (end of sequence) GGGTTTAGGGTTTAGGGTTTAGGGTTAGGGTTTAGGGTTTAGGGTTTTAG
h2tg000033l Forward (start of sequence) CCTAAACCCTGAAATCCCTATCCCTAAACCCTAACCCTAAACCCTAAACC
h2tg000035l Forward (start of sequence) CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
h2tg000037l Forward (start of sequence) TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
h2tg000039l Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
h2tg000047l Forward (start of sequence) TAACCCTAAACCTAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
h2tg000079l Forward (start of sequence) AAAACCCTAAACCCTAAACCCTAAACCCTAAAACCCTAAACCTCTAACCC
h2tg000082l Forward (start of sequence) CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCTAAACCCT
h2tg000098l Forward (start of sequence) CCCTAAACCCTAACCCTAAATACCCTAAACCCTAACCCCCTAAACCCTAA
h2tg000144l Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
h2tg000169l Forward (start of sequence) CCTAAACCTAAACCCTTAACCCTAAACCCTAAACCCTAAACCTCTAAACC
h2tg000188l Reverse (end of sequence) GGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGG
h2tg000220l Forward (start of sequence) CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
Telomeres found: 19 (16 forward, 3 reverse)Transposable element analysis
Hap 1
LTR recap
==================================================
file name: tmp_hap.fasta
sequences: 225
total length: 3093706697 bp (3093706697 bp excl N/X-runs)
GC level: 34.96 %
bases masked: 1728517665 bp ( 55.87 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 1962721 1728517665 bp 55.87 %
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: 1962721 1728517665 bp 55.87 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 291155 171016422 bp 5.53 %
Gypsy/DIRS1 615267 570505650 bp 18.44 %
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: 1728517665 bp 55.87 %
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 3093706697 0.0049 0.5541 0.89 6.52Hap 2
LTR recap
==================================================
file name: tmp_hap.fasta
sequences: 313
total length: 3104393956 bp (3104393956 bp excl N/X-runs)
GC level: 34.97 %
bases masked: 1782671732 bp ( 57.42 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 1963285 1782671732 bp 57.42 %
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: 1963285 1782671732 bp 57.42 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 214995 130467566 bp 4.20 %
Gypsy/DIRS1 586277 582670353 bp 18.77 %
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: 1782671732 bp 57.42 %
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 3104393956 0.0051 0.5696 0.89 6.52