ARANGS 2015

This is the git repository for the course Automated and Reproducible Analysis of Next Generation Sequencing (ARANGS 2015, timetable).

This repository contains source code, data, configuration files, documentation and reference materials.

Reference materials

DNA Sequencing Technologies http://www.nature.com/scitable/topicpage/DNA-Sequencing-Technologies-690
"A Quick Guide to Organizing Computational Biology Projects" http://dx.doi.org/10.1371/journal.pcbi.1000424
"A quick guide for developing effective bioinformatics programming skills." http://dx.doi.org/10.1371/journal.pcbi.1000589
"The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants" http://dx.doi.org/10.1093%2Fnar%2Fgkp1137
"A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies" http://dx.doi.org/10.1371/journal.pone.0017915
"A beginner's guide to eukaryotic genome annotation" http://dx.doi.org/10.1038/nrg3174
NGS glossary spreadsheet https://docs.google.com/spreadsheet/ccc?key=0Av8UW3JvZsgcdE9wZW1sYzlCQWFwNjBXLWMtQzZLN3c#gid=0
NGS platforms https://docs.google.com/document/pub?id=1rYbBPELjjezRVjkQfkulJI2jNxL5LsRuNXVv_CxCpd4
Unix Tutorials http://tldp.org/LDP/abs/html/ http://www.ee.surrey.ac.uk/Teaching/Unix/

SAM/BAM http://samtools.sourceforge.net/SAM1.pdf
VCF Format http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40
FASTQ http://maq.sourceforge.net/fastq.shtml
Sequence file formats http://bioinf.comav.upv.es/courses/sequence_analysis/sequence_file_formats.html