- Clone Jesse's conda-gcc5 repository and create an new environment
nanoflowwith GCC5 installed
git clone https://github.com/ressy/conda-gcc5.git
bash setup.py nanoflow- Clone this repository into a local directory and activate
nanoflowenvironment
git clone https://github.com/zhaoc1/nanoflow.git nanoflow
cd nanoflow
source activate nanoflow
conda install --file conda-requirements.txt- Clone Ryan Wick's Basecalling-comparison repository
mkdir local
cd local
git clone https://github.com/rrwick/Basecalling-comparison.git- Download other packages into local directory
## Nanopolish v0.9.0
git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
make
## Unicycler
git clone https://github.com/rrwick/Unicycler.git
cd Unicycler
python3 setup.py install
## set up for Quast
git clone https://github.com/lucian-ilie/E-MEM.git
cd E-MEM
make- Basecalling:
snakemake --configfile _all_basecalling- Preprocess: quality filter, confidently-binned, and subsampled subsample long reads
snakemake --configfile config.yml _all_preprocess- Hybrid assembly option 1: Canu + Nanopolish + Circlator + Pilon
snakemake --configfile config.yaml --cores 8 _all_draft1
## command to submit jobs to Respublica
snakemake -j 3 --configfile config.yml --cluster-config cluster.json -w 90 --notemp -p -c "qsub -cwd -r n -V -l h_vmem={cluster.h_vmem} -l m_mem_free={cluster.m_mem_free} -pe smp {threads}" _all_draft1-
Hybrid assembly option 2: Unicycler
depth=Xin the FASTA header: to preserve the relative depths. This is mainly used for plasmid sequences, which should be more represented in the reads than the chromosomal sequence.
snakemake --configfile config.yaml _all_draft2- Assembly assess and comparison
-
Metrics description
-
Misjoins: locations where two adjacent sequences in the assembly should be split apart and placed at distinct locations in order to match the reference. -
Relocation: a misjoin where a segments needs to be moved elsewhere on the chromosome. -
Misassemblies: QUAST categories misassemblies as either local (less than 1kbp discrepancy) or extensive (more than 1 kbp discrepancy)
-
-
A good reference guide for interpretting the dot plot is available here.
-
Some good tutorials:
-
Wish you knew sooner ๐
snakemake --configfile config.yaml _all_comp --use-conda- IGV: short/long reads mapped to draft assembly
snakemake --configfile config.yaml _all_map_igv- Generate bioinformatics report refer to
bioinfo_report.Rmd. An example output is shown inbioinfo_report.pdf.
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