MinION nanopore sequencing and assembly of a complete human papillomavirus genome: bioinformatics pipeline
A pipeline developed to analyse MinION sequencing data for the reconstruction of viral genomes
This pipeline was developed to analyse MinION sequencig raw data, to generate a consensus sequence for a viral genome. This script perform a polishing of the raw data and generate a de novo assemblig using Canu tool. After, it takes the canu contigs and performs a step of polishing using Medaka tool.
This pipe was written in python3 Guppy is required for the basecalling. Nanofilt and filtlong are required for the filtering of the reads. Canu is required for the assembling step. Medaka is required for the polishing step.
To run these scripts, each of the tools used needs to be installed before to launch the process.
Tools to install: Guppy, Nanofilt, Filtlong, Canu, Medaka.
Get Guppy from the MinION comunity and install it
conda install -c bioconda nanofilt
conda install -c bioconda filtlong
conda install -c bioconda canu
| Name | Example value | Description |
|---|---|---|
| --fast5_path | path/to/file | path to fast5 files |
| --flowcell | flowcell code | the code of flowcell used (ex. FLO-MIN106) |
| --kit | kit_used | the MinION kit used (ex. SQK-LSK109) |
| --threads | nr. of threads (int) | threads to be used (ex. 8) |
| --num | num_callers (int) | number of callers to use (ex. 8) |
| --barcode | barcode kit code | the code of the barcodes kit used (ex. EXP-PBC001 ) |
| --medaka_m | medaka model | define a model based on the basecaller (ex. r941_min_high_g303) - see medaka tool for more details - |
Flags are special parameters without value.
| Name | Description |
|---|---|
| -h | Display help |
Part5:
python3 MinION_pipe.py fast5_path flowcell kit threads num barcode medaka_m
| Name | Description | |
|---|---|---|
| Rosario Nicola Brancaccio | rosariobrancaccio@yahoo.it | Developer to contact for support |
| Massimo Tommasino | tommasinom@iarc.fr | |
| Tarik Gheit | gheitt@iartc.fr |
Rosario Nicola Brancaccio - (https://github.com/BioRB/)