A healthy taste of resources available, specifically for this course - not a comprehensive catalog.
...
- 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://cutadapt.readthedocs.io/en/stable/
- An excellent command line tool for adapter sequence removal
- Good support for trimming paired-end datasets
- Available at TACC at Anna's /work/01063/abattenh/local/bin/cutadapt
- Anna has an script that handles the details of paired-end read trimming:
- /work/01063/abattenh/code/script/align/trim_adapters.sh
- 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
...
- Comparison of different aligners
- by Heng Li, developer of BWA and MAQby Nils Homer, developer of BFAST
- File formats
- Aligners
- bwa (Burrows-Wheeler Aligner) by Heng Li – http://bio-bwa.sourceforge.net/
- fast, sensitive and easy to use
- bowtie2 – http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
- fast, sensitive and extremely configurable
- bwa (Burrows-Wheeler Aligner) by Heng Li – http://bio-bwa.sourceforge.net/
- Anna has some TACC-aware alignment scripts you might find useful
- bwa alignment
- /work/01063/abattenh/code/script/align/align_bwa_illumina.sh
- bowtie2 alignment
- /work/01063/abattenh/code/script/align/align_bowtie2_illumina.sh
- merging sorted BAM files (read-group aware)
- /work/01063/abattenh/code/script/align/merge_sorted_bams.sh
- email or come talk to me if you have questions or problems
- bwa alignment
...
- SAM (Sequence Alignment Map) format specification (pdf)
- Translate SAM file flags web calculator: http://broadinstitute.github.io/picard/explain-flags.html
- type in a decimal number to see which flags are set
- Translate SAM file flags web calculator: http://broadinstitute.github.io/picard/explain-flags.html
- samtools – http://samtools.sourceforge.net/ by Heng Li
- sam/bam conversion, flag filtering, sorting, indexing, duplicate filtering
- Picard toolkit – http://broadinstitute.github.io/picard/
- sam/bam utilities that are read-group aware
- especially MarkDuplicates for flagging duplicate alignments
- SAMStat - http://samstat.sourceforge.net/
- produces detailed graphical statistics for sam/bam files.
- bedtools – http://bedtools.readthedocs.org/en/latest/
- Swiss army knife for all manner of common bed, bam, vcf, gff file manipulation such as:
- intersecting bam or bed with annotation files
- bedtools intersect
- merging overlapping regions
- bedtools merge
- generation of per-base genome-wide signal in bedGraph format
- bedtools coverage
- bedtools multicov
- extracting fasta corresponding to regions
- bedtools getfasta
- intersecting bam or bed with annotation files
- Available in the TACC module system
- Swiss army knife for all manner of common bed, bam, vcf, gff file manipulation such as:
File formats and conversion
- SAM format specification – http://samtools.github.io/hts-specs/SAMv1.pdf
- crucial for performing format conversions, of which ChIP-seq analysis can have many
- Genome browser file formats – http://genome.ucsc.edu/FAQ/FAQformat.html
- BED, bedGraph, narrowPeak and many more
- SRA (Sequence Read Archive) from NCBI
- overview on this wiki
- SRA search home page
- SRA Toolkit
- UCSC file format conversion scripts - useful for getting to/from wig and bed to corresponding binary formats.
- Make sure you download the correct script for your operating system!
- A directory containing these tools can be found on stampede at /work/01063/abattenh/local/UCSC_utilities
- Mason program for simulating second-generation sequencing reads
...