...
- 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.
...
- The 1000 Genomes project - catalog of human genetic variants
- Tools
- Broad institute GATK - complex but powerful; used by 1000 Genomes
- File formats
- VCF (Variant Call Format) v4.0 - developed by 1000 Genomes project
Transcriptome analysis
- The Tuxedo pipeline: RNAseq with tophat/cufflinks
- tophat - exon-aware sequence alignment (uses bowtie)
- cufflinks - transcript assembly, differential expression & regulation
- RNAseq analysis protocol article in Nature Protocols
- cufflinks resource bundles for selected organisms (gff annotations, pre-built bowtie references, etc.)
...