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- Cheat sheet of useful Unix commands
- A funny SEQAnwers post about biologists starting to analyze NGS data
- http://seqanswers.com/forums/showthread.php?t=4589
Fastq analysis/manipulation
- 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 contaminant detection or adapter removal.
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