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flongle_actinomycetes_paper's Introduction

Scripts used in preparation of flongle actinomycetes paper.

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

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