Training

SEQUENCE READ ARCHIVE
The Next Generation Hands-on course will include units covering the EBI's Sequence Read Archive (SRA) service. One day will be spent specifically on the SRA and the SRA will be used as the source for data to be processed in the other hands-on sessions. Students can expect to become familiar with submission and retrieval formats for both metadata and data, submission pipelines and data retrieval using browser and webservices methods.

VELVET / CURTAIN
Velvet and Curtain are two complimentary tools that can be used for the assembly of genomes from next-generation sequence data. The session will consist of an introduction to both programs, followed by a hands-on exercise using short and long read data.

CORTEX
Cortex is a de Bruijn-based assembly and variant-calling framework capable of handling multiple deep sequenced large eukayote genomes simultaneously. Cortex supports short and long reads, even with next-generation error-rates. It is a coherent unified framework for assembling and genotyping variants across the size spectrum from SNPs to large variants, which can be used either with or without the assistance of a reference assembly. By implementing simultaneous analysis of multiple individuals Cortex can access both shared variation, and differences. Crucially, it provides a framework for directly understanding polymorphism in a diploid genome independently of a reference, more interestingly offers an alternative algorithm to the traditional alignment-based approaches for large insertion events by providing both a tool for detection and assembly for the novel sequences.

ChIP-SEQ DATA ANALYSIS
The goal of this hands-on session is to perform some basic tasks in the analysis of ChIP-seq data. We will find immuno-enriched areas using MACS and PeakAnalyzer utilities. We will visualize the data in a genome browser and perform annotation and motif analysis on the predicted binding regions.