A healthy taste of resources available, specifically for this course - not a comprehensive catalog.
Technology videos
Roche/454
Illumina (Solexa) Genome Analyzer and HiSeq
Life Technologies SOLiD
Pacific Biosciences
Community Resources
Getting started with Linux and Perl
Fastq analysis/manipulation
Alignment
- 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
- The 1000 Genomes project - catalog of human genetic variants
- Tools
- Broad institute GATK - complex but powerful; used by 1000 Genomes
- File formats
Transcriptome analysis
- The Tuxedo pipeline: RNAseq with tophat/cufflinks
Format converters and miscellaneous tools
- SRA (Sequence Read Archive) from NCBI
- Mason program for simulating second-generation sequencing reads.
De novo assembly
Other courses with online tutorials