Guppy Basecall and Demux process using Google Colab

khourious · Apr 21, 2024 · a088f1c · a088f1c
1 parent ea1c22d
commit a088f1c
Showing 1 changed file with 107 additions and 0 deletions.
diff --git a/google_colab/ont_guppy.ipynb b/google_colab/ont_guppy.ipynb
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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 Guppy (Oxford Nanopore Technologies)\n",
+        "\n",
+        "%%shell\n",
+        "\n",
+        "GUPPY_VERSION=6.5.7 # Archived Software\n",
+        "\n",
+        "wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_\"$GUPPY_VERSION\"_linux64.tar.gz -O ont-guppy.tar.gz\n",
+        "tar -vzxf ont-guppy.tar.gz; rm -rf ont-guppy.tar.gz\n",
+        "./ont-guppy/bin/guppy_basecaller --version"
+      ],
+      "metadata": {
+        "id": "dSavIZSzhTlP"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# Import Google Drive\n",
+        "\n",
+        "from google.colab import drive\n",
+        "drive.mount('/content/gdrive', force_remount=True)\n",
+        "\n",
+        "!ls gdrive/MyDrive"
+      ],
+      "metadata": {
+        "id": "i6QNwjcWlX7L"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# Basecall and Demultiplex process\n",
+        "\n",
+        "%%shell\n",
+        "\n",
+        "# Specify the name of the folder (i.e., 20240411_1608_MN22990_FAT84733_f175dd69/fast5)\n",
+        "DIR=\"20240411_1608_MN22990_FAT84733_f175dd69/fast5\"\n",
+        "\n",
+        "# Specify the barcode kit used for library preparation\n",
+        "BARKIT=\"EXP-NBD114\"\n",
+        "\n",
+        "PREFIX=\"$(echo \"$IDIR\" | awk -F/ '{print $1}')\"\n",
+        "\n",
+        "# Specify the accurate basecalling model - fast (fast), high (hac) or super (sup) accuracy\n",
+        "# dna_r9.4.1_450bps_fast.cfg\n",
+        "# dna_r9.4.1_450bps_hac.cfg\n",
+        "# dna_r9.4.1_450bps_sup.cfg\n",
+        "./ont-guppy/bin/guppy_basecaller -r --device cuda:0 --verbose_logs \\\n",
+        "-i \"$IDIR\" -s \"$PREFIX\"_GUPPY-BASECALL --min_qscore 8 \\\n",
+        "-c \"ont-guppy/data/dna_r9.4.1_450bps_fast.cfg\" \\\n",
+        "--gpu_runners_per_device 16 --cpu_threads_per_caller $(nproc)\n",
+        "\n",
+        "./ont-guppy/bin/guppy_barcoder -r --trim_adapters --barcode_kits \"$BARKIT\" \\\n",
+        "-i \"$PREFIX\"_GUPPY-FAST -s \"$PREFIX\"_GUPPY-DEMUX -t $(nproc)"
+      ],
+      "metadata": {
+        "id": "3h3DJ72AH1I9"
+      },
+      "execution_count": null,
+      "outputs": []
+    }
+  ]
+}