
# TIPPo assembly
2025-12-01 16:40:38	    131416 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.chloroplast.fasta.filter.800.round1.fasta.chloroplast.flye/assembly_graph.gfa ptDNA assembly graph GFA
2025-12-01 16:40:38	    313474 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.chloroplast.fasta.filter.800.round1.edge_3.edge_2.edge_1.organelle.chloroplast.fasta ptDNA assembly FASTA
2025-12-01 16:46:10	    375658 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.mitochondrial.fasta.filter.fasta.flye/assembly_graph.gfa mtDNA assembly graph GFA
2025-12-01 19:23:09	    113534 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.mitochondrial.fasta.filter.fasta.flye/assembly_graph.png mtDNA assembly graph Bandage PNG
2025-12-01 16:46:13	      9852 Breynia_androgyna/v5/0/summary-tippo.txt Run log memory and time
2025-12-01 16:41:03	      2096 Breynia_androgyna/v5/0/stdout-tippo.txt 
2025-12-01 16:46:13	      9852 Breynia_androgyna/v5/0/timing-tippo.txt 
2025-12-01 16:46:13	      9852 Breynia_androgyna/v5/0/memlog-tippo.txt

# Oatk assembly with -c 30
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-30.mito.gfa mtDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-30.mito.png mtDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-30.mito.ctg.fasta mtDNA assembly sequence FASTA
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-30.pltd.gfa ptDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-30.pltd.png ptDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-30.pltd.ctg.fasta ptDNA assembly sequence FASTA
2025-12-01 17:36:13	       454 Breynia_androgyna/v5/0/summary-oatk-30.txt Run log memory and time
2025-12-01 17:33:40	         0 Breynia_androgyna/v5/0/stdout-oatk-30.txt
2025-12-01 17:36:13	      4811 Breynia_androgyna/v5/0/memlog-oatk-30.csv
2025-12-01 17:36:13	      4649 Breynia_androgyna/v5/0/timing-oatk-30.txt

# Oatk assembly with -c 20
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-20.mito.gfa mtDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-20.mito.png mtDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-20.mito.ctg.fasta mtDNA assembly sequence FASTA
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-20.pltd.gfa ptDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-20.pltd.png ptDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-20.pltd.ctg.fasta ptDNA assembly sequence FASTA
2025-12-01 17:36:13	       454 Breynia_androgyna/v5/0/summary-oatk-20.txt Run log memory and time
2025-12-01 17:33:40	         0 Breynia_androgyna/v5/0/stdout-oatk-20.txt
2025-12-01 17:36:13	      4811 Breynia_androgyna/v5/0/memlog-oatk-20.csv
2025-12-01 17:36:13	      4649 Breynia_androgyna/v5/0/timing-oatk-20.txt

# Oatk assembly with -c 10
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-10.mito.gfa mtDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-10.mito.png mtDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-10.mito.ctg.fasta mtDNA assembly sequence FASTA
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-10.pltd.gfa ptDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-10.pltd.png ptDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-10.pltd.ctg.fasta ptDNA assembly sequence FASTA
2025-12-01 17:36:13	       454 Breynia_androgyna/v5/0/summary-oatk-10.txt Run log memory and time
2025-12-01 17:33:40	         0 Breynia_androgyna/v5/0/stdout-oatk-10.txt
2025-12-01 17:36:13	      4811 Breynia_androgyna/v5/0/memlog-oatk-10.csv
2025-12-01 17:36:13	      4649 Breynia_androgyna/v5/0/timing-oatk-10.txt

# HiMT assembly
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/himt/himt_chloroplast.gfa ptDNA assembly graph GFA 
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/himt/himt_chloroplast.png ptDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    378744 Breynia_androgyna/v5/0/himt/himt_mitochondrial.gfa mtDNA assembly graph GFA
2025-12-01 19:22:44	     97469 Breynia_androgyna/v5/0/himt/himt_mitochondrial.png mtDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    156727 Breynia_androgyna/v5/0/himt/chloroplast_path1.fa one form of ptDNA sequence
2025-12-01 19:15:22	    156727 Breynia_androgyna/v5/0/himt/chloroplast_path2.fa 2nd form of ptDNA sequence
2025-12-01 19:15:32	       492 Breynia_androgyna/v5/0/summary-himt.txt Run log memory and time
2025-12-01 19:15:28	     72228 Breynia_androgyna/v5/0/memlog-himt.csv
2025-12-01 19:15:32	      2713 Breynia_androgyna/v5/0/stdout-himt.txt
2025-12-01 19:15:32	      5900 Breynia_androgyna/v5/0/timing-himt.txt

# PMAT2 assembly
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_mt_main.gfa mtDNA assembly graph GFA
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_mt_main.png mtDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_pt_main.gfa ptDNA assembly graph GFA
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_pt_main.png ptDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_mt.fa mtDNA assembly sequence
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_pt.fa ptDNA assembly sequence
2025-12-01 19:15:32	       492 Breynia_androgyna/v5/0/summary-pmat2.txt Run log memory and time
2025-12-01 19:15:28	     72228 Breynia_androgyna/v5/0/memlog-pmat2.csv
2025-12-01 19:15:32	      2713 Breynia_androgyna/v5/0/stdout-pmat2.txt
2025-12-01 19:15:32	      5900 Breynia_androgyna/v5/0/timing-pmat2.txt

# example of summary-xxx.txt
summary-oatk.txt
Physical Memory Usage Summary:
Start used:      33549708 KB (32.00 GB)
Peak used:       42866308 KB (40.88 GB)
Net increase:    9316600 KB (8.89 GB)
Elapsed time:    00:23:42 (0.40 h)
Peak CPU load:   17.74
Start disk free: 483 GB
Min disk free:   459 GB
Disk used:       24 GB


# HiMT assessment on Oatk with -c 30
2025-12-01 19:21:24	   8713846 Breynia_androgyna/v5/0/assess/oatk-30/himt_mitochondrial.html HiMT assessment HTML
2025-12-01 19:21:33	      1748 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.spliced_genes.tsv
2025-12-01 19:21:33	       225 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:21:33	      2779 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.gene_integrity.tsv
2025-12-01 19:21:33	       200 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.mito_basic_info.tsv
2025-12-01 19:21:33	       142 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.contig_table.tsv
2025-12-01 19:21:33	       692 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.4c_metrics.tsv
2025-12-01 19:21:35	      9642 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.mito_qc_4c.pdf

# HiMT assessment on Oatk with -c 20
2025-12-01 19:21:45	   8713946 Breynia_androgyna/v5/0/assess/oatk-20/himt_mitochondrial.html
2025-12-01 19:21:53	      1748 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.spliced_genes.tsv
2025-12-01 19:21:53	       225 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:21:53	      2779 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.gene_integrity.tsv
2025-12-01 19:21:53	       200 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.mito_basic_info.tsv
2025-12-01 19:21:53	       142 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.contig_table.tsv
2025-12-01 19:21:53	       692 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.4c_metrics.tsv
2025-12-01 19:21:55	      9642 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.mito_qc_4c.pdf

# HiMT assessment on Oatk with -c 10
2025-12-01 19:22:04	   8713896 Breynia_androgyna/v5/0/assess/oatk-10/himt_mitochondrial.html
2025-12-01 19:22:13	      1748 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.spliced_genes.tsv
2025-12-01 19:22:13	       225 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:22:13	      2779 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.gene_integrity.tsv
2025-12-01 19:22:13	       200 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.mito_basic_info.tsv
2025-12-01 19:22:13	       142 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.contig_table.tsv
2025-12-01 19:22:13	       692 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.4c_metrics.tsv
2025-12-01 19:22:15	      9642 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.mito_qc_4c.pdf

# HiMT assessment on HiMT
2025-12-01 19:22:27	  12152219 Breynia_androgyna/v5/0/assess/himt/himt_mitochondrial.html
2025-12-01 19:22:36	      1231 Breynia_androgyna/v5/0/assess/himt/report/prefix.gene_integrity.tsv
2025-12-01 19:22:36	      1360 Breynia_androgyna/v5/0/assess/himt/report/prefix.spliced_genes.tsv
2025-12-01 19:22:36	       240 Breynia_androgyna/v5/0/assess/himt/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:22:36	       184 Breynia_androgyna/v5/0/assess/himt/report/prefix.mito_basic_info.tsv
2025-12-01 19:22:36	       413 Breynia_androgyna/v5/0/assess/himt/report/prefix.contig_table.tsv
2025-12-01 19:22:36	       692 Breynia_androgyna/v5/0/assess/himt/report/prefix.4c_metrics.tsv
2025-12-01 19:22:38	      9522 Breynia_androgyna/v5/0/assess/himt/report/prefix.mito_qc_4c.pdf

# HiMT assessment on TIPPo
2025-12-01 19:22:53	  15086214 Breynia_androgyna/v5/0/assess/tippo/himt_mitochondrial.html
2025-12-01 19:23:01	      1450 Breynia_androgyna/v5/0/assess/tippo/report/prefix.spliced_genes.tsv
2025-12-01 19:23:01	      1613 Breynia_androgyna/v5/0/assess/tippo/report/prefix.gene_integrity.tsv
2025-12-01 19:23:01	       228 Breynia_androgyna/v5/0/assess/tippo/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:23:01	       183 Breynia_androgyna/v5/0/assess/tippo/report/prefix.mito_basic_info.tsv
2025-12-01 19:23:01	       698 Breynia_androgyna/v5/0/assess/tippo/report/prefix.contig_table.tsv
2025-12-01 19:23:01	       681 Breynia_androgyna/v5/0/assess/tippo/report/prefix.4c_metrics.tsv
2025-12-01 19:23:03	      9479 Breynia_androgyna/v5/0/assess/tippo/report/prefix.mito_qc_4c.pdf

# HiMT assessment on PMAT2
2025-12-01 19:22:53	  15086214 Breynia_androgyna/v5/0/assess/pmat2/himt_mitochondrial.html
2025-12-01 19:23:01	      1450 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.spliced_genes.tsv
2025-12-01 19:23:01	      1613 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.gene_integrity.tsv
2025-12-01 19:23:01	       228 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:23:01	       183 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.mito_basic_info.tsv
2025-12-01 19:23:01	       698 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.contig_table.tsv
2025-12-01 19:23:01	       681 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.4c_metrics.tsv
2025-12-01 19:23:03	      9479 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.mito_qc_4c.pdf

# For each of these files, extract relevant information:

prefix.4c_metrics.tsv
prefix.contig_table.tsv
prefix.gene_integrity_summary.tsv
prefix.gene_integrity.tsv
prefix.mito_basic_info.tsv
prefix.spliced_genes.tsv
prefix.mito_qc_4c.pdf

# validation metrics for plant mitogenome assembly

term, definition, computation from HiMT assess results

# prefix.spliced_genes.tsv
gene    best_integrity  sum_integrity   nonzero_copies  min_exon_count_min      splice_type     canonical_trans_spliced model_length_bp best_orf_bp     cumulative_orf_bp       copy_integrities
nad5    72.0    99.0    2       1       trans   TRUE                            72.0,27.0,0.0,0.0
cox2    97.0    97.0    1       1       none    FALSE                           97.0,0.0,0.0,0.0
ccmB    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad9    100.0   123.0   3       2       none    TRUE                            100.0,12.0,11.0,0.0
atp6    100.0   130.0   3       2       none    FALSE                           100.0,17.0,13.0,0.0
nad1    57.0    161.0   4       2       trans   TRUE                            57.0,40.0,32.0,32.0
atp1    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad2    63.0    110.0   3       2       trans   TRUE                            63.0,37.0,10.0,0.0
cox1    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad6    100.0   107.0   2       2       none    FALSE                           100.0,7.0,0.0,0.0
cob     99.0    99.0    1       1       none    FALSE                           99.0,0.0,0.0,0.0
ccmFc   100.0   100.0   1       1       none    TRUE                            100.0,0.0,0.0,0.0
nad4    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
mttB    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
matR    100.0   200.0   2       2       none    FALSE                           100.0,100.0,0.0,0.0
nad7    100.0   131.0   4       2       none    TRUE                            100.0,11.0,10.0,10.0
atp8    100.0   117.0   2       2       none    FALSE                           100.0,17.0,0.0,0.0
atp9    100.0   124.0   2       2       none    FALSE                           100.0,24.0,0.0,0.0
nad3    100.0   167.0   2       2       none    FALSE                           100.0,67.0,0.0,0.0
ccmC    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
cox3    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad4L   100.0   200.0   2       2       none    FALSE                           100.0,100.0,0.0,0.0
atp4    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
ccmFN   100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0

# prefix.contig_table.tsv
Index   Contig name     Conserved gene number   GC content      Length  Depth
1       edge_223        10      0.45    330338  62
2       edge_72 11      0.45    264628  58
3       edge_217        10      0.45    137611  51
4       edge_224        4       0.45    119506  55
5       edge_216        8       0.45    115730  56
6       edge_1  0       0.46    1414    93

prefix.contig_table.tsv This is parsed from the HiMT “Contig information” table.
- Index
- Contig name
- Conserved gene number (how many conserved mitochondrial protein-coding genes are found on that contig)
- GC content
- Length
- Depth

# prefix.gene_integrity_summary.tsv
metric  value
genes_total     24
genes_present   24
genes_missing   0
genes_high_integrity_ge95       21
geneset_completeness_prop       1.0
high_integrity_gene_prop        0.875
mean_best_integrity     95.33333333333333
median_best_integrity   100.0

# prefix.gene_integrity.tsv
gene    copy    integrity
nad5    copy1   72.0
nad5    copy2   27.0
nad5    copy3   0.0
nad5    copy4   0.0
cox2    copy1   97.0
cox2    copy2   0.0
cox2    copy3   0.0
cox2    copy4   0.0
ccmB    copy1   100.0
ccmB    copy2   0.0
ccmB    copy3   0.0
ccmB    copy4   0.0
nad9    copy1   100.0
nad9    copy2   12.0
nad9    copy3   11.0
nad9    copy4   0.0
...
...
...

# prefix.mito_basic_info.tsv
metric  value
Total length    969227
Total contig number     6
N count 0
Number of closed circular contigs       0
Total GC content        0.45
Minimum length  1414
Maximum length  330338
N50     264628

Extract:
- GC content

# prefix.4c_metrics.tsv
category        metric  value   description
completeness    genes_total     24      Total genes
completeness    genes_present   24      Present genes
completeness    geneset_completeness_prop       1.0     Proportion present
completeness    mean_best_integrity     0.9533333333333333      Mean best integrity
completeness    median_best_integrity   1.0     Median best integrity
contiguity      num_contigs     6       # contigs
contiguity      total_length    969227  total length
contiguity      N50     264628  N50
consistency     frac_spliced_genes      0.125   Fraction spliced (cis+trans)
consistency     frac_trans_spliced_among_spliced        1.0     Among spliced, fraction trans
consistency     frac_canonical_trans_spliced_detected   0.5     Detected canonical trans-spliced

Extract:
- geneset completeness proportion
- total length
- number of contigs
- N50

# 4C metrics

1. Completeness: Core gene completeness: geneset completeness proportion

2. CONTIGUITY

Available directly from mito_basic_info.tsv:
- Total contig number
- N50
- Maximum contig
- Minimum contig
- Total length
- L50: number of contigs whose cumulative sum reaches half the genome length
- Genome fragmentation index = 1 – (N50 / total_length)
- Largest contig proportion = max_len / total_length

3. Correctness: n/a

4. Comprehensiveness

Coefficient of variation (CV): CV = sd(lengths) / mean(lengths)


# Auto

Now, create a new polap-bash-hifi-make-manifest.sh by copying polap-bash-make-manifest.sh. Edit polap-bash-hifi-make-manifest.sh so that you add 4 items for assembly results: Consider these to add entries for oatk, tippo, himt, pmat2 assembly results files. Leave other code in the script as is. As we did before, if files are missing, add empty items so we avoid errors missing.

Each entry needs items for mtdna gfa, mtdna fasta, mtdna png, and these three things for ptdna as well.
for each assembly entry, parse summary-xxx.txt to extract: Net increase as used memory, Elapsed time for used run time, Disk used: for disk usage. for memory and time extract two different format or unit.
memory KB and GB. time 00:xx:xx and 0.40 h like format.

Each assembly entry needs items for HiMT assessment as well. Consider content below:

we need 4C values:

# 4C metrics

1. Completeness: Core gene completeness: geneset completeness proportion

2. CONTIGUITY

Available directly from mito_basic_info.tsv:

* Total contig number
* N50
* Maximum contig
* Minimum contig
* Total length
* L50: number of contigs whose cumulative sum reaches half the genome length
* Genome fragmentation index = 1 – (N50 / total_length)
* Largest contig proportion = max_len / total_length

3. Correctness: n/a

4. Comprehensiveness

Coefficient of variation (CV): CV = sd(lengths) / mean(lengths)

These are files related to store as entries and extract from;

# TIPPo assembly

2025-12-01 16:40:38	    131416 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.chloroplast.fasta.filter.800.round1.fasta.chloroplast.flye/assembly_graph.gfa ptDNA assembly graph GFA
2025-12-01 16:40:38	    313474 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.chloroplast.fasta.filter.800.round1.edge_3.edge_2.edge_1.organelle.chloroplast.fasta ptDNA assembly FASTA
2025-12-01 16:46:10	    375658 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.mitochondrial.fasta.filter.fasta.flye/assembly_graph.gfa mtDNA assembly graph GFA
2025-12-01 19:23:09	    113534 Breynia_androgyna/v5/0/tippo/SRR25111202.fastq.mitochondrial.fasta.filter.fasta.flye/assembly_graph.png mtDNA assembly graph Bandage PNG
2025-12-01 16:46:13	      9852 Breynia_androgyna/v5/0/summary-tippo.txt Run log memory and time
2025-12-01 16:41:03	      2096 Breynia_androgyna/v5/0/stdout-tippo.txt
2025-12-01 16:46:13	      9852 Breynia_androgyna/v5/0/timing-tippo.txt
2025-12-01 16:46:13	      9852 Breynia_androgyna/v5/0/memlog-tippo.txt

# Oatk assembly with -c 30

2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-30.mito.gfa mtDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-30.mito.png mtDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-30.mito.ctg.fasta mtDNA assembly sequence FASTA
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-30.pltd.gfa ptDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-30.pltd.png ptDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-30.pltd.ctg.fasta ptDNA assembly sequence FASTA
2025-12-01 17:36:13	       454 Breynia_androgyna/v5/0/summary-oatk-30.txt Run log memory and time
2025-12-01 17:33:40	         0 Breynia_androgyna/v5/0/stdout-oatk-30.txt
2025-12-01 17:36:13	      4811 Breynia_androgyna/v5/0/memlog-oatk-30.csv
2025-12-01 17:36:13	      4649 Breynia_androgyna/v5/0/timing-oatk-30.txt

# Oatk assembly with -c 20

2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-20.mito.gfa mtDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-20.mito.png mtDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-20.mito.ctg.fasta mtDNA assembly sequence FASTA
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-20.pltd.gfa ptDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-20.pltd.png ptDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-20.pltd.ctg.fasta ptDNA assembly sequence FASTA
2025-12-01 17:36:13	       454 Breynia_androgyna/v5/0/summary-oatk-20.txt Run log memory and time
2025-12-01 17:33:40	         0 Breynia_androgyna/v5/0/stdout-oatk-20.txt
2025-12-01 17:36:13	      4811 Breynia_androgyna/v5/0/memlog-oatk-20.csv
2025-12-01 17:36:13	      4649 Breynia_androgyna/v5/0/timing-oatk-20.txt

# Oatk assembly with -c 10

2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-10.mito.gfa mtDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-10.mito.png mtDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-10.mito.ctg.fasta mtDNA assembly sequence FASTA
2025-12-01 17:36:11	    388412 Breynia_androgyna/v5/0/oatk/oatk-10.pltd.gfa ptDNA assembly graph GFA
2025-12-01 19:21:41	    127312 Breynia_androgyna/v5/0/oatk/oatk-10.pltd.png ptDNA assembly graph Bandage PNG
2025-12-01 17:36:11	    399707 Breynia_androgyna/v5/0/oatk/oatk-10.pltd.ctg.fasta ptDNA assembly sequence FASTA
2025-12-01 17:36:13	       454 Breynia_androgyna/v5/0/summary-oatk-10.txt Run log memory and time
2025-12-01 17:33:40	         0 Breynia_androgyna/v5/0/stdout-oatk-10.txt
2025-12-01 17:36:13	      4811 Breynia_androgyna/v5/0/memlog-oatk-10.csv
2025-12-01 17:36:13	      4649 Breynia_androgyna/v5/0/timing-oatk-10.txt

# HiMT assembly

2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/himt/himt_chloroplast.gfa ptDNA assembly graph GFA
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/himt/himt_chloroplast.png ptDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    378744 Breynia_androgyna/v5/0/himt/himt_mitochondrial.gfa mtDNA assembly graph GFA
2025-12-01 19:22:44	     97469 Breynia_androgyna/v5/0/himt/himt_mitochondrial.png mtDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    156727 Breynia_androgyna/v5/0/himt/chloroplast_path1.fa one form of ptDNA sequence
2025-12-01 19:15:22	    156727 Breynia_androgyna/v5/0/himt/chloroplast_path2.fa 2nd form of ptDNA sequence
2025-12-01 19:15:32	       492 Breynia_androgyna/v5/0/summary-himt.txt Run log memory and time
2025-12-01 19:15:28	     72228 Breynia_androgyna/v5/0/memlog-himt.csv
2025-12-01 19:15:32	      2713 Breynia_androgyna/v5/0/stdout-himt.txt
2025-12-01 19:15:32	      5900 Breynia_androgyna/v5/0/timing-himt.txt

# PMAT2 assembly

2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_mt_main.gfa mtDNA assembly graph GFA
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_mt_main.png mtDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_pt_main.gfa ptDNA assembly graph GFA
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_pt_main.png ptDNA assembly graph Bandage PNG
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_mt.fa mtDNA assembly sequence
2025-12-01 19:15:22	    131339 Breynia_androgyna/v5/0/pmat2/gfa_result/PMAT_pt.fa ptDNA assembly sequence
2025-12-01 19:15:32	       492 Breynia_androgyna/v5/0/summary-pmat2.txt Run log memory and time
2025-12-01 19:15:28	     72228 Breynia_androgyna/v5/0/memlog-pmat2.csv
2025-12-01 19:15:32	      2713 Breynia_androgyna/v5/0/stdout-pmat2.txt
2025-12-01 19:15:32	      5900 Breynia_androgyna/v5/0/timing-pmat2.txt

# example of summary-xxx.txt

summary-oatk.txt
Physical Memory Usage Summary:
Start used:      33549708 KB (32.00 GB)
Peak used:       42866308 KB (40.88 GB)
Net increase:    9316600 KB (8.89 GB)
Elapsed time:    00:23:42 (0.40 h)
Peak CPU load:   17.74
Start disk free: 483 GB
Min disk free:   459 GB
Disk used:       24 GB

# HiMT assessment on Oatk with -c 30

2025-12-01 19:21:24	   8713846 Breynia_androgyna/v5/0/assess/oatk-30/himt_mitochondrial.html HiMT assessment HTML
2025-12-01 19:21:33	      1748 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.spliced_genes.tsv
2025-12-01 19:21:33	       225 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:21:33	      2779 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.gene_integrity.tsv
2025-12-01 19:21:33	       200 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.mito_basic_info.tsv
2025-12-01 19:21:33	       142 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.contig_table.tsv
2025-12-01 19:21:33	       692 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.4c_metrics.tsv
2025-12-01 19:21:35	      9642 Breynia_androgyna/v5/0/assess/oatk-30/report/prefix.mito_qc_4c.pdf

# HiMT assessment on Oatk with -c 20

2025-12-01 19:21:45	   8713946 Breynia_androgyna/v5/0/assess/oatk-20/himt_mitochondrial.html
2025-12-01 19:21:53	      1748 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.spliced_genes.tsv
2025-12-01 19:21:53	       225 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:21:53	      2779 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.gene_integrity.tsv
2025-12-01 19:21:53	       200 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.mito_basic_info.tsv
2025-12-01 19:21:53	       142 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.contig_table.tsv
2025-12-01 19:21:53	       692 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.4c_metrics.tsv
2025-12-01 19:21:55	      9642 Breynia_androgyna/v5/0/assess/oatk-20/report/prefix.mito_qc_4c.pdf

# HiMT assessment on Oatk with -c 10

2025-12-01 19:22:04	   8713896 Breynia_androgyna/v5/0/assess/oatk-10/himt_mitochondrial.html
2025-12-01 19:22:13	      1748 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.spliced_genes.tsv
2025-12-01 19:22:13	       225 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:22:13	      2779 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.gene_integrity.tsv
2025-12-01 19:22:13	       200 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.mito_basic_info.tsv
2025-12-01 19:22:13	       142 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.contig_table.tsv
2025-12-01 19:22:13	       692 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.4c_metrics.tsv
2025-12-01 19:22:15	      9642 Breynia_androgyna/v5/0/assess/oatk-10/report/prefix.mito_qc_4c.pdf

# HiMT assessment on HiMT

2025-12-01 19:22:27	  12152219 Breynia_androgyna/v5/0/assess/himt/himt_mitochondrial.html
2025-12-01 19:22:36	      1231 Breynia_androgyna/v5/0/assess/himt/report/prefix.gene_integrity.tsv
2025-12-01 19:22:36	      1360 Breynia_androgyna/v5/0/assess/himt/report/prefix.spliced_genes.tsv
2025-12-01 19:22:36	       240 Breynia_androgyna/v5/0/assess/himt/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:22:36	       184 Breynia_androgyna/v5/0/assess/himt/report/prefix.mito_basic_info.tsv
2025-12-01 19:22:36	       413 Breynia_androgyna/v5/0/assess/himt/report/prefix.contig_table.tsv
2025-12-01 19:22:36	       692 Breynia_androgyna/v5/0/assess/himt/report/prefix.4c_metrics.tsv
2025-12-01 19:22:38	      9522 Breynia_androgyna/v5/0/assess/himt/report/prefix.mito_qc_4c.pdf

# HiMT assessment on TIPPo

2025-12-01 19:22:53	  15086214 Breynia_androgyna/v5/0/assess/tippo/himt_mitochondrial.html
2025-12-01 19:23:01	      1450 Breynia_androgyna/v5/0/assess/tippo/report/prefix.spliced_genes.tsv
2025-12-01 19:23:01	      1613 Breynia_androgyna/v5/0/assess/tippo/report/prefix.gene_integrity.tsv
2025-12-01 19:23:01	       228 Breynia_androgyna/v5/0/assess/tippo/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:23:01	       183 Breynia_androgyna/v5/0/assess/tippo/report/prefix.mito_basic_info.tsv
2025-12-01 19:23:01	       698 Breynia_androgyna/v5/0/assess/tippo/report/prefix.contig_table.tsv
2025-12-01 19:23:01	       681 Breynia_androgyna/v5/0/assess/tippo/report/prefix.4c_metrics.tsv
2025-12-01 19:23:03	      9479 Breynia_androgyna/v5/0/assess/tippo/report/prefix.mito_qc_4c.pdf

# HiMT assessment on PMAT2

2025-12-01 19:22:53	  15086214 Breynia_androgyna/v5/0/assess/pmat2/himt_mitochondrial.html
2025-12-01 19:23:01	      1450 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.spliced_genes.tsv
2025-12-01 19:23:01	      1613 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.gene_integrity.tsv
2025-12-01 19:23:01	       228 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.gene_integrity_summary.tsv
2025-12-01 19:23:01	       183 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.mito_basic_info.tsv
2025-12-01 19:23:01	       698 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.contig_table.tsv
2025-12-01 19:23:01	       681 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.4c_metrics.tsv
2025-12-01 19:23:03	      9479 Breynia_androgyna/v5/0/assess/pmat2/report/prefix.mito_qc_4c.pdf

# For each of these files, extract relevant information:

prefix.4c_metrics.tsv
prefix.contig_table.tsv
prefix.gene_integrity_summary.tsv
prefix.gene_integrity.tsv
prefix.mito_basic_info.tsv
prefix.spliced_genes.tsv
prefix.mito_qc_4c.pdf

# validation metrics for plant mitogenome assembly

term, definition, computation from HiMT assess results

# prefix.spliced_genes.tsv

gene    best_integrity  sum_integrity   nonzero_copies  min_exon_count_min      splice_type     canonical_trans_spliced model_length_bp best_orf_bp     cumulative_orf_bp       copy_integrities
nad5    72.0    99.0    2       1       trans   TRUE                            72.0,27.0,0.0,0.0
cox2    97.0    97.0    1       1       none    FALSE                           97.0,0.0,0.0,0.0
ccmB    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad9    100.0   123.0   3       2       none    TRUE                            100.0,12.0,11.0,0.0
atp6    100.0   130.0   3       2       none    FALSE                           100.0,17.0,13.0,0.0
nad1    57.0    161.0   4       2       trans   TRUE                            57.0,40.0,32.0,32.0
atp1    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad2    63.0    110.0   3       2       trans   TRUE                            63.0,37.0,10.0,0.0
cox1    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad6    100.0   107.0   2       2       none    FALSE                           100.0,7.0,0.0,0.0
cob     99.0    99.0    1       1       none    FALSE                           99.0,0.0,0.0,0.0
ccmFc   100.0   100.0   1       1       none    TRUE                            100.0,0.0,0.0,0.0
nad4    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
mttB    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
matR    100.0   200.0   2       2       none    FALSE                           100.0,100.0,0.0,0.0
nad7    100.0   131.0   4       2       none    TRUE                            100.0,11.0,10.0,10.0
atp8    100.0   117.0   2       2       none    FALSE                           100.0,17.0,0.0,0.0
atp9    100.0   124.0   2       2       none    FALSE                           100.0,24.0,0.0,0.0
nad3    100.0   167.0   2       2       none    FALSE                           100.0,67.0,0.0,0.0
ccmC    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
cox3    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
nad4L   100.0   200.0   2       2       none    FALSE                           100.0,100.0,0.0,0.0
atp4    100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0
ccmFN   100.0   100.0   1       1       none    FALSE                           100.0,0.0,0.0,0.0

# prefix.contig_table.tsv

Index   Contig name     Conserved gene number   GC content      Length  Depth
1       edge_223        10      0.45    330338  62
2       edge_72 11      0.45    264628  58
3       edge_217        10      0.45    137611  51
4       edge_224        4       0.45    119506  55
5       edge_216        8       0.45    115730  56
6       edge_1  0       0.46    1414    93

prefix.contig_table.tsv This is parsed from the HiMT “Contig information” table.

* Index
* Contig name
* Conserved gene number (how many conserved mitochondrial protein-coding genes are found on that contig)
* GC content
* Length
* Depth

# prefix.gene_integrity_summary.tsv

metric  value
genes_total     24
genes_present   24
genes_missing   0
genes_high_integrity_ge95       21
geneset_completeness_prop       1.0
high_integrity_gene_prop        0.875
mean_best_integrity     95.33333333333333
median_best_integrity   100.0

# prefix.gene_integrity.tsv

gene    copy    integrity
nad5    copy1   72.0
nad5    copy2   27.0
nad5    copy3   0.0
nad5    copy4   0.0
cox2    copy1   97.0
cox2    copy2   0.0
cox2    copy3   0.0
cox2    copy4   0.0
ccmB    copy1   100.0
ccmB    copy2   0.0
ccmB    copy3   0.0
ccmB    copy4   0.0
nad9    copy1   100.0
nad9    copy2   12.0
nad9    copy3   11.0
nad9    copy4   0.0
...
...
...

# prefix.mito_basic_info.tsv

metric  value
Total length    969227
Total contig number     6
N count 0
Number of closed circular contigs       0
Total GC content        0.45
Minimum length  1414
Maximum length  330338
N50     264628

Extract:

* GC content

# prefix.4c_metrics.tsv

category        metric  value   description
completeness    genes_total     24      Total genes
completeness    genes_present   24      Present genes
completeness    geneset_completeness_prop       1.0     Proportion present
completeness    mean_best_integrity     0.9533333333333333      Mean best integrity
completeness    median_best_integrity   1.0     Median best integrity
contiguity      num_contigs     6       # contigs
contiguity      total_length    969227  total length
contiguity      N50     264628  N50
consistency     frac_spliced_genes      0.125   Fraction spliced (cis+trans)
consistency     frac_trans_spliced_among_spliced        1.0     Among spliced, fraction trans
consistency     frac_canonical_trans_spliced_detected   0.5     Detected canonical trans-spliced

Extract:

* geneset completeness proportion
* total length
* number of contigs
* N50

# 4C metrics

1. Completeness: Core gene completeness: geneset completeness proportion

2. CONTIGUITY

Available directly from mito_basic_info.tsv:

* Total contig number
* N50
* Maximum contig
* Minimum contig
* Total length
* L50: number of contigs whose cumulative sum reaches half the genome length
* Genome fragmentation index = 1 – (N50 / total_length)
* Largest contig proportion = max_len / total_length

3. Correctness: n/a

4. Comprehensiveness

Coefficient of variation (CV): CV = sd(lengths) / mean(lengths)

