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