Recovery of small plasmid sequences via Oxford Nanopore sequencing

This repository supplements our paper: Wick RR, Judd LM, Wyres KL, Holt KE. Recovery of small plasmid sequences via Oxford Nanopore sequencing. Microbial Genomics. 2021. doi:10.1099/mgen.0.000631.

Figures

The figures directory contains all figures (both main-text and supplementary) for the study, in PDF and PNG formats. Enter that directory to see its README with captions for each of the figures.

Method

The method.md file contains the commands I ran to conduct the analysis.

Scripts

The scripts directory contains Python scripts I wrote for the analysis: align_reads.py, assign_reads.py, depth_and_gc.py, get_depths.py, get_gc.py and read_start_counts.py. See the header in each script for more information on how it works, and see the method.md file for how I used these to produce the data in the study.

Tables

The Table_S1.xlsx file contains various stats at the run level, barcode level and replicon level. See the first worksheet in the file for a more detailed description of the content.

Plots

The plots.Rmd file contains the R code used to generate plots for the figures.

Data

The reads, assemblies and per-read tables are too large for GitHub, so you can download them from here: bridges.monash.edu/articles/dataset/Small_plasmid_Nanopore_data/13543754

There you will find these files:

• tech_rep_1_ligation_reads.tar: a FASTQ file and sequencing summary file for the first ligation run
• tech_rep_1_rapid_reads.tar: a FASTQ file and sequencing summary file for the first rapid run
• tech_rep_1_illumina_reads.tar: separate paired-end FASTQ files for each of the seven isolates in the first replicate
• tech_rep_2_ligation_reads.tar: a FASTQ file and sequencing summary file for the second ligation run
• tech_rep_2_rapid_reads.tar: a FASTQ file and sequencing summary file for the second ligation run
• tech_rep_2_illumina_reads.tar: separate paired-end FASTQ files for each of the seven isolates in the second replicate
• assemblies.tar.gz: reference assemblies for the seven isolates (FASTA format)
• read_tables.tar: the TSV output of assign_reads.py (one line per read) for each of the four sequencing runs