Managing bioinformatics software and pipelines (IN-PERSON)

PrerequisitesNew

Setting up a computer for running bioinformatic analysis can be a challenging process. Most bioinformatic applications involve the use of many different software packages, which are often part of long data processing pipelines. In this course we will teach you how to overcome these challenges by using package managers and workflow management software.

We will have examples of software and pipelines for processing different types of data (RNA-seq, ChIP-seq, variant calling and viral genomes), making this course appealing to researchers working in a wide range of applications.

However, please note that we will not cover the details of any specific type of bioinformatic analysis. The idea of this course is to introduce the computational tools to get your work done, not to teach how those tools work. We will also not teach you how to write your own pipelines, or create your own software containers, but rather on how to use existing tools to boost your bioinformatic analysis.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.
• Guidance on visiting Cambridge and finding accommodation is available here.

• Researchers who are starting to run bioinformatics analysis on their own.
• Attendees of our training courses on specific applications (e.g. RNA-seq, ChIP-seq, variant calling, etc.) will greatly benefit from this course.
• HPC users who would like to learn how to manage software and automate and parallelise analyses using available pipelines.

Essential:

• A working knowledge of the UNIX command line is essential (course registration page).
  • If you are not able to attend this prerequisite course, please work through our Unix command line materials ahead of the course (up to section 6).
• Basic understanding of high-throughput sequencing technologies.
  • Watch this iBiology video for an excellent overview.

Preferable:

• A knowledge of how to work on a HPC server using SLURM (course registration page). If you don't know how to work on a HPC, you will struggle to follow the last session of the course.
• A general knowledge the data processing steps for at least one "omics" application (e.g. RNA-seq, ChIP-seq, variant calling, bacterial genomics, metagenomics, etc.).

Number of sessions: 1

During the course you will learn about:

• The utility of package managers in bioinformatics.
• How package managers can be used to create and maintain complex software environments.
• How containerisation solutions can be used to solve the problem of software dependencies.
• Install, configure and run automated analysis pipelines developed and maintained by the bioinformatics community.

By the end of this course, you will be able to:

• Recognise when you should use package managers, software containers and workflow managers in your bioinformatic analyses.
• Create software environments using conda/mamba.
• Search for and use software images to launch commands within a container using singularity.
• Search for bioinformatic workflows from the nf-core community and use their documentation to configure your analysis.
• Use nextflow to execute those workflows both on a local computer as well as a remote HPC server.

Presentations, demonstrations and practicals

Participants can make use of the computers in the training room.

Under development

• Free for registered University of Cambridge students
• £ 60/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 120/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

1

several times a year

• Introduction to the Unix command line (ONLINE LIVE TRAINING)