Create for a multiplex input must to add a file genome_size.csv with size of each genome (bp) per barcode. :
e.g
barcode,genome_size
barcode01,3000000
barcode02,4500000
barcode03,5000000
barcode04,4000000
barcode05,3200000
barcode06,3500000
The optimal number of polishing rounds is determined automatically using the CART algorithm. The prediction is based on multiple parameters, including error rate, N50/L50, genome coverage, Total Length of Matches, Average Occurrences, Distinct Minimizers, and processing time per round.
| Source | Parameter | Description |
|---|---|---|
| Minimap2 | DistinctMinimizers | Number of unique minimizers found (Minimap2 value),change < 0.1% in distinct minimizers |
| AverageOccurrences | Average occurrences of minimizers (Minimap2),change < 0.01 in average occurrences | |
| TotalLengthMatches | Total length of aligned matches,change < 0.1% | |
| ProcessingTime | Total execution time per round (Racon or Minimap2), change < 5% | |
| RACON | Processing Time | Change < 5% |
| QUAST | N50/L50 | Minimum contig length that covers 50% of the assembly, change < 100 bp |
| QUAST/MEDAKA | ErrorRate | Error rate in the sequence after each polishing round |
| BUSCO | Completeness (BUSCO) | Change < 1% in complete genes |
| Target Value | Optional Rounds | Optimal number of rounds needed to achieve convergence |
nextflow run main.nf --mode assemble --genome_size_file barcode_info.csv -profile <docker/singularity/conda>
--mode : assemble / hybrid_amr / hybrid_vc -profile:
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