Dataset Open Access

Training material for the course "Exome analysis with GALAXY"

Uva, Paolo; Cuccuru, Gianmauro

Galaxy is an open source, web-based platform for data intensive biomedical research. It makes accessible bioinformatics applications to users lacking programming skills, enabling them to easily build analysis workflows for NGS data.
 
The course "Exome analysis using Galaxy" is aimed at PhD student, biologists, clinicians and researchers who are analysing, or need to analyse in the near future, high throughput exome sequencing data. The aim of the course is to make participants familiarise with the Galaxy platform and prepare them to work independently, using state-of-the art tools for the analysis of exome sequencing data.

The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the strategies for the analysis of exome next-generation experiments, starting from the raw sequence data. Analyses include sequence quality control, alignment to a reference genome, refinement of aligned sequences, variant calling, annotation and interpretation, and tools for visual inspection of results. Participants will apply the knowledge gained during the course to the analysis of Illumina’s real exome datasets, and implement workflows to reproduce the complete analysis. After the course, participants will be able to create pipeline for their individual analyses.

Those are the needed datasets for this course.

Files (5.9 GB)
Name Size
dbsnp_138.hg19.chr8.vcf
md5:3147fb92a21d33209e28a6bf1c2df1f9
571.5 MB Download
dbsnp_138.hg19.chr8.vcf.gz
md5:7bde6f2f49d4b4de396017ce68ef8503
77.4 MB Download
father_R1.fq
md5:c4bb7d614766247814a1f87a6d242164
506.9 MB Download
father_R1.fq.gz
md5:c96c18f947dacf82998b9dc633f8aa42
150.8 MB Download
father_R2.fq
md5:ba863a68cd6c8aab78fd06631d2f1b96
506.9 MB Download
father_R2.fq.gz
md5:c6385922291206a84ca6c4e8454ad653
148.1 MB Download
hg19_chr8.fa
md5:45e729d7bfac3fde174f1368f4d9a685
149.3 MB Download
hg19_chr8.fa.gz
md5:c8d7dc7f4c796af3b09364c097e4661a
46.9 MB Download
mapped_reads_father.bam
md5:8f19e9482d9a583f13eba61364b3c1ff
353.3 MB Download
mapped_reads_mother.bam
md5:029e5c6601e9a38b1434b295e574edb4
310.5 MB Download
mapped_reads_proband.bam
md5:73f9ebdba67ce0827b7ffc6f37a709b2
410.7 MB Download
mother_R1.fq
md5:868542038099ac56fc6fad13bbaf4b3d
444.9 MB Download
mother_R1.fq.gz
md5:958b4888517c4b3df277f12c3f6b6c22
132.9 MB Download
mother_R2.fq
md5:ce235e1b5a737206378e6862a19bc47d
444.9 MB Download
mother_R2.fq.gz
md5:0c5022de981db7a56b01d693524ba28d
130.6 MB Download
NexteraRapidCaptureExpandedExome_Probes.hg19.chr8.HybridSelection
md5:dcb4921c090c00f6a2193cadd506672b
707.4 kB Download
NexteraRapidCaptureExpandedExome_Target.hg19.chr8.HybridSelection
md5:930f58091b6af6c29ee33a5d748f366f
385.9 kB Download
NexteraRapidCaptureExpandedExome_Target.hg19.chr8.padding200.bed
md5:bdbbcd46e154be5d756075edecfe90b3
372.1 kB Download
Pedigree.txt
md5:be8690f273e7fb29ecb1dd7a8cf2e818
68 Bytes Download
proband_R1.fq
md5:0c28ac556c491fa61b48ec7c96f3181d
599.3 MB Download
proband_R1.fq.gz
md5:1e0703c3d70f62011a18aa418046643a
174.0 MB Download
proband_R2.fq
md5:a5e98a44f8dd1f3f00980606f0c568e9
599.3 MB Download
proband_R2.fq.gz
md5:e95b6609ee459d5c6e653ba1c3322848
173.5 MB Download
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