Corrects plasmid sequences for unconfirmed clones using nanopore sequence and annotates
First clone the repo, make sure you're in a sensible directory:
git clone https://github.com/osilander/clone-correct.git
Move into the clone-correct directory:
cd clone-correct
Open the data directory and replace the fastq file with fastq file(s) of your own. These need to be named with the suffix .fastq; the prefix will be used to name the result folders. Replace the reference .fasta file with the reference file that you wish to correct. This sequence can have any name, and is used to create an alignment of the new corrected (polished) sequence. Note that by default this will align all the .fastq files to thsi single reference. If you have more than one reference then you will need to repeat these steps once for each reference.
The output of this should be a set of directories, one for each barcode. In each there will be an annotated .gbk file with the sequence and annotations of the corrected clone (pLasmid_pLann.gbk), an interactive .html file containing a plasmid map (pLasmid_pLann.html), an alignment of the reference and corrected sequence (ending in .aln), the new consensus sequence (consensus.fasta), and a few extraneous files that might be removed with a clean rule in future iterations. The step by step installations below will hopefully prevent system OS conflicts when using a conda .yaml.
Please ignore the steps for which you already have the software installed.
(1) install conda, see here https://docs.conda.io/en/latest/miniconda.html
(2) install mamba:
conda install -c conda-forge mamba
(3) install snakemake:
mamba install -c bioconda snakemake
(4) Create a new environment for the analysis:
conda create -n medaka
conda activate medaka
(5) install medaka
mamba install -c bioconda medaka
(6) install mafft, filtlong, plannotate:
mamba install -c bioconda mafft
mamba intstall -c bioconda filtlong
mamba install -c bioconda plannotate
(87 First invoke dry-run of snakemake to check the steps, then invoke snakemake then get a snakemake reports:
snakemake -np
# two threads (-j 2)
snakemake -p -j 2
snakemake --report report.html