Bioinformatics Software Lab 2019
Location: MTZ Seminar Room, Pauwelstr, 19; 3rd Floor, Corridor B room 3.04.
Dates: Monday 9:30-12:30 (starting 16.04.2017)
Prerequisite (desirable): Introduction to Bioinformatics
Credits: 7 (10 with extra work for Media M.Sc. Students)
Lecturers: Ivan G. Costa
Evaluation: 20% prototypes / 60% final project / 20% presentation
RWTH online description: Bioinformatik Praktikum
Next-generation sequencing (NGS) allows the measurement of molecular characteristics of individuals on a genome-wide scale. The application of NGS methods to large patient groups enables precise medicine, i.e. finding genetic features to guide medical treatment. The low level analysis of NGS data imposes large computational and statistical challenges. NGS data are typically large (1 to 100 GB per sample/patient) requiring efficient computational strategies for data analysis and storage. Moreover, NGS data contains artifacts and noise, which affects the reliability of predictions and leads to errors.
In this software lab, we will explore computational problems associated to the analysis of nanopore sequencing data. Nanopore represent a novel sequencing technology allowing sequencing experiments to be done at home and with a laptop. However, the high error rates requires robust computational methods to perform base calling detection and align the reads to genomes. Students will implement strategies based on machine learning and statistical methods to analyze nanopore sequencing data. We will use the high-performance cluster and GPUs from the ITC RWTH Aachen as the computational platform for this course.
29.04.2019 –Introduction to Bioinformatics and Next Generation Sequencing
06.05.2018 – Practical Course in NGS data analysis
07.05.2018 – Project Description
13.05.2018 – Introduction to HPC clusters and GPUs
20.05.2018 – Project Development
14.05.2018 to 8.07.2018 – Project Development
15.07.2019 – Project Presentation
Literature & Videos
Check for Chapter 9 for some algorithms on short read alignment http://bioinformaticsalgorithms.com/videos.htm