A healthy taste of resources available, specifically for this course - not a comprehensive catalog.
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- Wikipedia FASTQ format page
- Illumina library construction on GSAF user wiki - useful for contaminant detection or adapter removal
- FastQC from Babraham Bioinformatics ; – http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- produces nice quality report for fastq files
- cutadapt – https://code.google.Cutadapt - com/p/cutadapt/
- An excellent command line tool for adapter sequence removal
- Good support for trimming paired-end datasets
- Available at TACC only at Anna's /work/01063/abattenh/local/bin/cutadapt
- documentation at https://codecutadapt.google.com/p/cutadapt/wiki/documentation
- trimmomatic – http://www.usadellab.org/cms/?page=trimmomatic
- Supports trimming paired-end datasets. I haven't used it but it seems to be popular.
- fastx toolkit – http://hannonlab.cshl.edu/fastx_toolkit/
- Command line tools for fastq analysis and manipulation
- Good for hard clipping. Available at TACC.
- Documentation at: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
Alignment and aligners
- Jeff Barrick's introduction to NGS presentation
- Comparison of different aligners
- by Heng Li, developer of BWA and MAQ
- by Nils Homer, developer of BFAST
- Aligners
- bwa - fast, sensitive and easy to use
- bowtie2 - fast, sensitive, configurable, easy to use
- bowtie (http://bowtie-bio.sourceforge.net/index.shtml) - 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
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
- BEDTools manual on readthedocs.org
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