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

Technology videos

Illumina (Solexa) Genome Analyzer and HiSeq
Life Technologies SOLiD
Pacific Biosciences

Community Resources

Getting started with Linux and Perl

Fastq analysis/manipulation


  • Comparison of different aligners
  • 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)

Alignment analysis

  • SAM (Sequence Alignment Map) format specification (pdf)
  • sam/bam tools
    • samtools - sam/bam conversion, flag filtering, bam sort/index
    • Picard - sam/bam utilities that are read-group aware
    • Translate SAM file flags - type in a decimal number to see which flags are set
  • SAMstat - produces detailed graphical statistics for sam/bam files.
  • BEDTools - region overlap, merge, coverage & much more, w/bed, bam, vcf, gff support

UCSC Genome Browser

Variant calling

Transcriptome analysis

Format converters and miscellaneous tools

De novo assembly

  • <put something here>

Other courses with online tutorials

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