mvdenbog/MPXV_NanoPoreSeq

code accompanying "Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic" # MPXV_NanoPoreSeq This is snakefile code accompanying "Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic". Vandenbogaert M, Kwasiborski A, Gonofio E, Descorps-Declère S, Selekon B, Nkili Meyong AA, Ouilibona RS, Gessain A, Manuguerra JC, Caro V, Nakoune E, Berthet N. Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic. Sci Rep. 2022 Jun 24;12(1):10768. doi: 10.1038/s41598-022-15073-1. PMID: 35750759; PMCID: PMC9232561. ncbi.nlm.nih.gov ## Installation & Usage ### Installation Using Docker/Singularity. All conda/python dependencies are defined in accompanying dependency files: - `conda_installed_packages_base.txt` - `conda_installed_packages_homopolish.txt` - `pip38_installed_packages.txt` The provided Singularity file is illustrative of the dependency definitions, and on building a target docker/singularity instance. ## Preparation of data ### Basecalling Input data is supposed to be basecalled, prior to using the provided snakemake file. Example basecalling instructions (below instructions are uinsg Guppy v 3.2.4, and are indicative only): Example using CPUs: ``` dir=/opt/Guppy/ont-guppy-cpu_3.4.4/ont-guppy-cpu/bin ${dir}/guppy_basecaller --kit ${kit} --flowcell ${flowcell} --barcode_kits ${barcode_kit} -i ${indir}/ -s ${outdir} --num_callers 4 --cpu_threads_per_caller 20 -q 4000 --qscore_filtering --min_qscore ${min_qscore} --disable_pings --trim_barcodes ``` Example using GPUs: Works on Tesla P100 only. ``` ${dir}/guppy_basecaller -i /data/fast5_pass/ --save_path /scratch/out/ --flowcell ${flowcell} --kit ${barcode_kit} --gpu_runners_per_device 8 -r --qscore_filtering --min_qscore 7 -x auto --disable_pings --trim_barcodes ``` ### Organization of FASTQ files and reference genome (here reference NC_003310). Working directory will be `/scratch/`. ``` cd /scratch/ ln ~/RawData/*.fastq . l …