Dependencies:
All require Python 3, please see software sources for more detailed requirements. I recommend installing
all of these inside the Medaka conda environment. Samtools and minimap2 already installed with Medaka environment.
Medaka
Prefered installation - Using conda environment, takes care of medaka dependencies:
conda create -n medaka -c conda-forge -c bioconda medaka
conda activate medaka
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virtualenv medaka --python=python3 --prompt "(medaka) "
. medaka/bin/activate
pip install medaka
Source: https://github.com/nanoporetech/medaka
NanoFilt
One of several available long read filtering softwares, NanoFilt has the advantage of specifying
the maximimum read length which is good for filtering out extra long reads.
pip install nanofilt
pip install nanofilt --upgrade
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conda install -c bioconda nanofilt
Source: https://github.com/wdecoster/nanofilt
Samtools
Minimap2
Integrative Genomics Browser - IGV
Specify --igv path/to/igv.sh to take screenshots of alignments.
Biopython
Used for IO and marker based binning.
Source: https://biopython.org/wiki/Download
Emboss
Needle pairwise alignments for consensus alignments.
Source: http:https://emboss.sourceforge.net/download/
BulkPlasmidSeq usage examples:
For binning sequences based on unique sequences in reference - biobin:
python bulkPlasmidSeq.py biobin -i path/to/reads -r path/to/plasmids -o output_directory
For generating concensus sequences - medaka:
python bulkPlasmidSeq.py medaka -i my_reads.fastq -r my_plasmid_genome.fa -o output_directory -t 4
Filter reads with nanofilt.
python bulkPlasmidSeq.py medaka --filter \
-i unfiltered_reads.fastq \
-r my_plasmid_genome.fa \
-q 7 \
-o output_directroy