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Dorado Basecall and Demux process using Google Colab
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{ | ||
"nbformat": 4, | ||
"nbformat_minor": 0, | ||
"metadata": { | ||
"colab": { | ||
"provenance": [], | ||
"gpuType": "T4" | ||
}, | ||
"kernelspec": { | ||
"name": "python3", | ||
"display_name": "Python 3" | ||
}, | ||
"language_info": { | ||
"name": "python" | ||
}, | ||
"accelerator": "GPU" | ||
}, | ||
"cells": [ | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"metadata": { | ||
"id": "gxcweSl4fmRz" | ||
}, | ||
"outputs": [], | ||
"source": [ | ||
"# Initiate GPU runtime\n", | ||
"\n", | ||
"import tensorflow as tf\n", | ||
"tf.test.gpu_device_name()\n", | ||
"\n", | ||
"import torch\n", | ||
"torch.cuda.get_device_name(0)\n", | ||
"\n", | ||
"!rm -rf sample_data" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"source": [ | ||
"# Install Dorado (Oxford Nanopore Technologies)\n", | ||
"\n", | ||
"%%shell\n", | ||
"\n", | ||
"DORADO_VERSION=0.6.0 # Updated 02 Apr 2024\n", | ||
"\n", | ||
"pip install pod5\n", | ||
"\n", | ||
"wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-\"$DORADO_VERSION\"-linux-x64.tar.gz -O dorado.tar.gz\n", | ||
"tar -vzxf dorado.tar.gz; rm -rf dorado.tar.gz; mv dorado-\"$DORADO_VERSION\"-linux-x64 ont-dorado\n", | ||
"./ont-dorado/bin/dorado download --directory ont-dorado/models\n", | ||
"./ont-dorado/bin/dorado --version" | ||
], | ||
"metadata": { | ||
"id": "dSavIZSzhTlP" | ||
}, | ||
"execution_count": null, | ||
"outputs": [] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"source": [ | ||
"# Import Google Drive\n", | ||
"\n", | ||
"from google.colab import drive\n", | ||
"drive.mount('/content/gdrive', force_remount=True)\n", | ||
"\n", | ||
"!ls gdrive/MyDrive" | ||
], | ||
"metadata": { | ||
"id": "i6QNwjcWlX7L" | ||
}, | ||
"execution_count": null, | ||
"outputs": [] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"source": [ | ||
"# Basecall and Demultiplex process\n", | ||
"\n", | ||
"%%shell\n", | ||
"\n", | ||
"# Specify the name of the folder (i.e., 20240411_1608_MN22990_FAT84733_f175dd69/fast5)\n", | ||
"DIR=\"20240411_1608_MN22990_FAT84733_f175dd69/fast5\"\n", | ||
"\n", | ||
"# Specify the barcode kit used for library preparation\n", | ||
"BARKIT=\"EXP-NBD114\"\n", | ||
"\n", | ||
"PREFIX=\"$(echo \"$IDIR\" | awk -F/ '{print $1}')\"\n", | ||
"\n", | ||
"pod5 convert fast5 $IDIR --output \"/content/gdrive/MyDrive/\"$PREFIX\".pod5\"\n", | ||
"\n", | ||
"# Specify the accurate basecalling model - fast (fast), high (hac) or super (sup) accuracy\n", | ||
"# dna_r9.4.1_e8_fast@v3.4\n", | ||
"# dna_r9.4.1_e8_hac@v3.3\n", | ||
"# dna_r9.4.1_e8_sup@v3.3\n", | ||
"./ont-dorado/bin/dorado basecaller \"ont-dorado/models/dna_r9.4.1_e8_sup@v3.3\" \\\n", | ||
"\"/content/gdrive/MyDrive/\"$PREFIX\".pod5\" -r --min-qscore 8 --emit-fastq >> \"/content/gdrive/MyDrive/\"$PREFIX\"_DORADO-BASECALL.fastq\"\n", | ||
"\n", | ||
"./ont-dorado/bin/dorado demux \"/content/gdrive/MyDrive/\"$PREFIX\"_DORADO-SUP.fastq\" --emit-fastq \\\n", | ||
"--output-dir \"/content/gdrive/MyDrive/\"$PREFIX\"_DORADO-DEMUX\" --kit-name $BARKIT -t $(nproc)" | ||
], | ||
"metadata": { | ||
"id": "3h3DJ72AH1I9" | ||
}, | ||
"execution_count": null, | ||
"outputs": [] | ||
} | ||
] | ||
} |