Source code, data, documentation and reference materials
- "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
- "Managing Projects with GNU Make." http://oreilly.com/catalog/make3/book/index.csp
- "Advanced Bash-Scripting Guide" http://tldp.org/LDP/abs/html/
- NGS glossary https://docs.google.com/spreadsheet/ccc?key=0Av8UW3JvZsgcdE9wZW1sYzlCQWFwNjBXLWMtQzZLN3c#gid=0
- NGS platforms https://docs.google.com/document/pub?id=1rYbBPELjjezRVjkQfkulJI2jNxL5LsRuNXVv_CxCpd4
- Data analysis Perl scripts http://wiki.bioinformatics.ucdavis.edu/index.php/Data_Analysis
- DNA Sequencing Technologies http://www.nature.com/scitable/topicpage/DNA-Sequencing-Technologies-690
- SAM/BAM http://samtools.sourceforge.net/SAM1.pdf
- Binary sequence trace formats. http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#ztr
- 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
- "A Closer Look At The First PacBio Sequence Dataset" http://oelemento.wordpress.com/2011/01/03/a-closer-look-at-the-first-pacbio-sequence-dataset/
- "First look at Ion Torrent data: De novo assembly" http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/
- "Introduction to the processing of short read next generation sequencing data" http://darrenjw.wordpress.com/2010/11/28/introduction-to-the-processing-of-short-read-next-generation-sequencing-data/
- "A quick introduction to the Bioconductor ShortRead package for the analysis of NGS data" http://darrenjw.wordpress.com/2010/11/29/a-quick-introduction-to-the-bioconductor-shortread-package-for-the-analysis-of-ngs-data/
- "2012 NGS Field Guide � Overview" http://www.molecularecologist.com/next-gen-fieldguide/
- "Maq, BWA, and Bowtie Compared" http://massgenomics.org/2009/07/maq-bwa-and-bowtie-compared.html
- Short Read Aligner comparison http://massgenomics.org/short-read-aligners
- samtools http://samtools.sourceforge.net/
- BWA http://bio-bwa.sourceforge.net/
- sff2fastq https://github.com/indraniel/sff2fastq
- fastqc http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- picard http://picard.sourceforge.net/
- bowtie http://bowtie-bio.sourceforge.net/
- maq http://maq.sourceforge.net/
- velvet http://www.ebi.ac.uk/~zerbino/velvet/
- prinseq http://prinseq.sourceforge.net/
- bfast http://bfast.sourceforge.net/
- mira http://mira-assembler.sourceforge.net/
- vcftools http://vcftools.sourceforge.net/
- BioRuby bio-ngs https://github.com/helios/bioruby-ngs/
- BioPerl https://github.com/bioperl/bioperl-live/
- BioConductor http://www.bioconductor.org/
- BioPython https://github.com/biopython/biopython/
- FAST-X toolkit http://hannonlab.cshl.edu/fastx_toolkit/
- GATK http://www.broadinstitute.org/gatk/
- BioLib https://github.com/biolib/biolib
- SOAP http://soap.genomics.org.cn/index.html
- CLC workbench http://www.clcbio.com/
- Geneious http://www.geneious.com/
- mothur http://www.mothur.org/wiki/Main_Page
- BioClipse http://www.bioclipse.net/
- git http://git-scm.com/ (github setup: https://help.github.com/)
- perl http://www.perl.org/
- python http://python.org/
- ruby http://www.ruby-lang.org/en/
- r http://www.r-project.org/
- Galaxy http://galaxy.psu.edu/
- Taverna http://www.taverna.org.uk/
- SeqAnswers http://seqanswers.com/
- BioStar http://www.biostars.org/
- myExperiment http://www.myexperiment.org/
- Short read mapping http://www.youtube.com/watch?v=1ZyoI-4ObSA
- Adding a simple galaxy service http://www.youtube.com/watch?v=d-fDngweW-M
- Taxonomic placement of metagenomic data (orchid mycorrhiza)
- Alignment against reference genome (plasmodium)
- Comparative analysis of multicellular genomic data