I would suggest the most recent workshop organized by Lex Nederbragt @ University of Oslo Fall 2014

Course website: https://wiki.uio.no/projects/clsi/index.php/INF-BIOX121_H14

Genome assembly part: https://github.com/lexnederbragt/INF-BIOx121_fall2014_de_novo_assembly

Lex's blog about the workshop: http://flxlexblog.wordpress.com/2014/11/04/on-the-benefits-of-open-for-teaching/

A few genome assemblers used in the workshop:

• Assembly using Velvet on MiSeq data
• Assembly using HGAP on PacBio data
• Assembly using SPAdes on a combined Illumina PE + Oxford Nanopore MinION data

I guess Titus Brown's workshop in Michigan, US could be a good choice if you're OK with the travel. Details here: http://bioinformatics.msu.edu/ngs-summer-course-2015

I don't know if it can be considered as workshop, but there's a great course on Coursera that has a chapter or two on genome assembly.

Bioinformatics Algorithms (Part 1)

It's quite challenging, I found.

Hi,

We are planing a practical hands-on NGS course for beginners. It looks like it'll be one week in early March 2015.

Our plan:

Monday: Linux Introduction (command line usage, piping and redirecting, first command line programming, Introduction to R)

Tuesday and Wednesday: NGS Introduction (notations, file formats, QC, mapping, mapping statistics, visualization, etc.)

Thursday and Friday: Choice between 1) model organism (detect standard and non-standard transcripts, quantify exons/genes/isoforms, find differentially expressed genes) and 2) non-model organism (create genome and transcriptome assembly, quantify expressed regions/contigs, find differentially expressed regions/contigs, find out what genes the diff. expressed region/contigs belong to)

The final date/agenda will be online within the next days on our website: www.ecseq.com

Best,
David

Check our upcoming hands-on bioinformatics workshop 'De Novo Genome Assembly Using Next-Generation Sequence Data'