Main text figures:
| Figure no. | Description | File |
|---|---|---|
| 1 | Effect of sequencing coverage | src/plot_assembly_quality.R |
| 2 | Sequencing run details | src/sequencing_qc.R |
| 3 | Assembly stats | src/plot_assembly_qc_sample.R |
| 4 | CDPS | src/QTOF/postdereplication_prism.R |
| 5 | lassopeptide | src/QTOF/ga6002_lassopeptide.R |
| 6 | MiBiG BGCs BLAST | src/QTOF/postdereplication_mibig.R |
Supplementary figures:
| Figure no. | Description | File |
|---|---|---|
| S1 | Genome sizes JGI | src/avg_genome_sizes.R.R |
| S2 | Coverage and contig edge | src/plot_assembly_quality.R |
| S3 | Read length and assm quality | src/plot_assembly_qc_readlen.R |
| S4 | Read length and contig edge | src/plot_assembly_qc_readlen.R |
| S6 | taxonomy and BGC | src/16s.R |
| S7 | GNPS spectra | src/QTOF/postdereplication_gnps.R |
| S10 | aminocoumarin BGC | src/plot_cluster_aminocoumarin.R |
Parameters for primary analyses:
| Analysis | File |
|---|---|
| Base calling | src/guppy.sh |
| Demultiplexing | src/qcat.sh |
| Assembly | src/canu.sh |
| Assembly polishing | src/racon.sh and medaka.sh |
| AntiSMASH | src/antismash.sh |