Content Comparison

A healthy taste of resources available, specifically for this course - not a comprehensive catalog.

Sequencing Technologies

• Paper comparing NGS technologies (Liu et al., 2012)
• Broad Center GA Boot Camp

• Technology videos

  • Roche/454

  • Illumina (Solexa) Genome Analyzer and HiSeq

  • Life Technologies SOLiD

  • Pacific Biosciences

Community Resources

• SEQAnwers forum - many NGS sequencing questions answered here
• UCSC Genome Browser - visualize and download NGS data (see more below)
• Galaxy website for online sequencing data analysis
• Broad Institute Integrated Genomcs Viewer (IGV) - especially good for bam files

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• Wikipedia FASTQ format page
• FastQC from Babraham Bioinformatics; produces nice quality report for fastq files.
• Cutadapt - An excellent command line tool for adapter sequence removal.
• FASTX Toolkit - Command line tools for fastq analysis and manipulation
• Illumina library construction on GSAF user wiki - useful for contaminent detection or adapter removal.

Alignment and aligners

• Jeff Barrick's introduction to NGS presentation
  • Image Added
• Comparison of different aligners
  • by Heng Li, developer of BWA and MAQ
  • by Nils Homer, developer of BFAST
• Aligners
  • bowtie (http:bowtie-bio.sourceforge.net/) - very fast, not very sensitive
  • BFAST wiki & manual - slow and relatively complicated, but tunable sensitivity
  • bwa - fast, sensitive and easy to use
  • bowtie2 - fast, sensitive, configurable, easy to use
• File formats
  • fastq format
  • The SAM (Sequence Alignment Map) format specification (pdf)

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