--- a
+++ b/exseek/templates/summarize_cutadapt_se.ipynb
@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pylab inline"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "from IPython.display import display\n",
+    "\n",
+    "def gradient_func(val):\n",
+    "    return '<span style=\"background: linear-gradient(90deg, #d65f5f {0}%, transparent 0%)\">{0:.3f}</span>'.format(val)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "summary = pd.read_table('cutadapt.txt', sep='\\t', index_col=0)\n",
+    "summary_reads = summary.loc[:, ['total_reads', 'reads_with_adapters', 'reads_too_short', 'reads_kept']]\n",
+    "display(summary_reads.style.set_caption('Reads summary'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "percent_reads = 100.0*summary_reads.div(summary_reads['total_reads'], axis=0)\n",
+    "percent_reads.drop(columns=['total_reads'], inplace=True)\n",
+    "display(percent_reads.style.format(gradient_func).set_caption('Reads percentage'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "summary_bp = summary.loc[:, ['total_bp', 'bp_quality_trimmed', 'bp_kept']]\n",
+    "display(summary_bp.style.set_caption('Base pairs summary'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "percent_bp = 100.0*summary_bp.div(summary_bp['total_bp'], axis=0)\n",
+    "percent_bp.drop(columns=['total_bp'], inplace=True)\n",
+    "display(percent_bp.style.format(gradient_func).set_caption('Base pairs percentage'))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.6"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": false
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}