Ready-to-use workflow for long read assembly

Reconciling with multiple assemblers, e.g., Canu and Flye.

Rapid assembly soly with a trusted assembler i.e., Flye.

Installation

Make sure conda is installed. Miniconda is enough for the whole pipeline.

Install latest version of mamba and snakemake, and activate the conda environment to run snakemake.

conda install -n base -c conda-forge mamba
mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

Usage

Manually edit the working directory path and params in the config.yaml.

Sample Initialization

mkdir /path/to/working/directory
python init.py -p /path/to/raw/data -o /path/to/working/directory

/path/to/raw/data shall be the main directory containing respective runs. E.g. /mnt/md0/metapredict/raw,

/mnt/md0/metapredict/raw
├── RAPID19
│   └── basecalled_fq
│       ├── barcode01
│       ├── barcode02
│       ├── barcode03
│       ├── barcode04
│       ├── barcode05
│       ├── barcode06
│       ├── barcode07
│       └── barcode08
├── RAPID20
│   └── basecalled_fq
│       ├── barcode06
│       ├── barcode07
│       ├── barcode08
│       ├── barcode09
│       ├── barcode10
│       ├── barcode11
│       └── barcode12

All (assembly + pangenome)

snakemake all -j 24 --use-conda --config work_dir=/path/to/working/directory

Assembly

snakemake assemble -j 24 --use-conda --config work_dir=/path/to/working/directory

Pangenome

snakemake pangenome -j 24 --use-conda --config work_dir=/path/to/working/directory

Variants calling

snakemake -j 6 --use-conda /mnt/md0/nano_snp/out_dh5a/results/variants/vcfs_isc_merged.ann.vcf --config work_dir="/mnt/md0/nano_snp/out_dh5a"