Output Files

Output Files Explanation

The output directory generated by PMAT autoMito contains the following structure:

output_dir/
├── assembly_result/
│   ├── PMATAllContigs.fna       # Raw assembly contigs generated by the core engine
│   └── PMATContigGraph.txt      # Contig adjacency and connection graph
├── gfa_result/
│   ├── PMAT_mt_raw.gfa          # Initial mitogenome assembly graph (GFA1 format)
│   ├── PMAT_mt_main.gfa         # Optimized and filtered mitogenome graph
│   ├── PMAT_mt.fa               # Final reconstructed mitogenome sequence (FASTA)
│   ├── PMAT_pt_raw.gfa          # Initial chloroplast assembly graph (GFA1 format)
│   ├── PMAT_pt_main.gfa         # Optimized and filtered chloroplast graph
│   └── PMAT_pt.fa               # Final reconstructed chloroplast sequence (FASTA)
├── gkmer_result/
│   ├── gkmer_histo.txt          # Kmer frequency distribution histogram
│   └── summary.txt              # Estimated genome size and coverage statistics
├── subsample/
│   └── PMAT_cut_seq.fa          # Subsampled sequencing reads used for assembly
└── PMAT_orgAss.txt              # Quality evaluation and completeness assessment report

Assembly Assessment Report (PMAT_orgAss.txt)

This report provides an automated quality evaluation of the assembled organellar genome based on conserved protein-coding genes:

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             Mitochondrial Assembly Assessment             
 ==========================================================

 Basic Statistics:
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 Total contigs:          1   
 Total length:           99.8 kb
 Average depth:          5.4 x
 Total genes found:      22/24 (91.7%)
 Duplicated contigs:     0   

 Per-contig Details:
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 Contig ID   Genes     Gene List           
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 1           22        atp1,atp4,atp6,at...
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