Content Comparison

A healthy taste of resources available, specifically for this course - not a comprehensive catalog.

Community Resources

...

Linux/TACC

• Linux fundamentals on this wiki
• Wikis for the 3 CBRS Unix/Linux workshops:
  • Introduction to Unix
  • Intermediate Unix
  • Advanced Bash scripting

• Online tutorials:

  • Ryan's Linux Tutorial: http://ryanstutorials.net/linuxtutorial/
  • Unix bootcamp for biologists: http://korflab.ucdavis.edu/bootcamp.html
  • Unix primer (longer version) for biologists:
    • http://korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v2.3.4.pdf

Community Resources

• UCSC Genome Browser - visualize and download NGS data (see more below)
• Galaxy website for online sequencing data analysis
• Broad Institute Integrated Genomcs Genomics Viewer (IGV) -
  
  • especially good for
  bam files2012 Next-Gen Sequence Analysis Workshop (Michigan State University) has similar tutorials to our course
  • also includes introductions to using visualizing BAM file details
• Introduction to Sequence analysis in the Amazon EC2 cloud
  Paper
  • where you can "rent" Linux machines (useful if you don't have access to TACC or BRCF pods)
  • Python, R, ChIP-Seq, etc.maintained mRNA-seq protocols from this workshop here

Sequencing Technologies

• Galaxy website for online sequencing data analysis
• SEQAnwers forum - many NGS sequencing questions answered here
  • A funny SEQAnwers post about biologists starting to analyze NGS data: http://seqanswers.com/forums/showthread.php?t=4589

Sequencing Technologies

• Overviews
  
  • Wikipedia overview of NGS technologies
  • Broad Center GA Boot Camp
  • Early paper comparing NGS technologies (Liu et al., 2012)
  Broad Center GA Boot Camp

• Technology

videos

• intros

  • Illumina (Solexa)
Genome Analyzer and HiSeq
• • – most common "short" (< 300 bp) read sequencing
    

    • Short Illumina video

    • Longer Illumina video
    • 2016 Sequencing Technologies talk
  • Newer single molecule sequencing
    • Oxford Nanopore
    • PacBio SMRT system
  • Single cell sequencing
    • 10x Genomics platforms
  • Older technologies (not common now)
    

    • Life Technologies SOLiD (short reads in "colorspace")

    • Roche/454

• Pacific Biosciences

...

• • • – long (multi-Kb) reads often used in assemblies

FASTQ analysis/manipulation/QC

• 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 FASTQ files
• MultiQC – http://multiqc.info/
  
  • A great tool for consolidating QC multiple QC reports into one HTML page
  • Anna's Byte Club tutorial on using MultiQC – https://utexas.atlassian.net/wiki/display/bioiteam/Using+MultiQC
• cutadapt – https://codecutadapt.googlereadthedocs.comio/pen/cutadaptstable/
  • 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://cutadapt.readthedocs.org/en/stable/
  • Script that handles the details of paired-end read trimming
    
    • /work2/projects/BioITeam/common/script/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 Suite of command line tools for fastq FASTQ and FASTA analysis and manipulation
  • Good for hard clipping. Available at TACC., FASTA file manipulations
  • Documentation at: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

Alignment and aligners

• 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
• File formats
• fastq format
The seqtk– https://github.com/lh3/seqtk
• Suite of command line tools for FASTQ and FASTA analysis and manipulation

Reference genomes

• Gencode – https://www.gencodegenes.org/
  
  • reference genomes, transcriptomes and high-quality annotations for human and mouse
• UCSC downloads – http://hgdownload.cse.ucsc.edu/downloads.html
  • reference genomes, transcriptomes and high-quality annotations for many eukaryotes
• Ensembl downloads – http://ftp.ensembl.org/pub
  
  • reference genomes, transcriptomes and high-quality annotations for many eukaryotes
• NCBI
  
  • RefSeq – https://www.ncbi.nlm.nih.gov/refseq/
    • well curated genome, transcriptome sequences
  • GenBank – https://www.ncbi.nlm.nih.gov/genbank/
    • public repository for sequence data, especially for prokaryotic genomes
    • not curated
• Reference genome vocabulary – https://software.broadinstitute.org/gatk/documentation/article?id=7857
  • excellent introduction to the types of genome references and the vocabulary used to describe them
    • aimed at higher eukaryotes but vocabulary useful nonetheless
• GATK blog describing ALT contigs in GRCh38 – https://software.broadinstitute.org/gatk/blog?id=8180
• Support for mapping to ALT contigs containing variants
  
  • bwa mem + bwakit by Heng-Li – https://github.com/lh3/bwa/blob/master/README-alt.md

Basic alignment and aligners

• File formats
  • input: FASTQ format
  • output: 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
  • BEDTools manual on readthedocs.org

...

• • • SAM1.pdf – header fields, body fields, flag definitions
    • https://github.com/samtools/hts-specs/blob/master/SAMtags.pdf – tag fields
• 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
• samtools – http://samtools.sourceforge.net/
  • also by Heng Li
• Picard toolkit – http://broadinstitute.github.io/picard/
• bedtools – http://bedtools.readthedocs.org/en/latest/
  
  • Swiss army knife for all manner of common BED/BAM file manipulation such as:
    • region filtering
    • generation of per-base genome-wide signal (bedGraph)
    • intersecting peaks with annotation files
    • extracting fasta corresponding to regions
• Anna
  • • fast, sensitive and extremely configurable
• Comparison of different aligners
  • by Heng Li, developer of bwa, samtools, and many other bioinformatics tools
• The BioITeam has some TACC-aware alignment scripts you might find useful:
  • bwa alignment
    • /work/01063projects/abattenhBioITeam/codecommon/script/align/align_bwa_illumina.sh
  • bowtie2 alignment
    • /work/01063projects/abattenhBioITeam/codecommon/script/align/align_bowtie2_illumina.sh
  • merging sorted BAM files (read-group aware)
    
    • /work/01063projects/abattenhBioITeam/codecommon/script/align/merge_sorted_bams.sh
  • kallisto pseudo-alignment to annotated transcripts
    • /work/projects/BioITeam/common/script/run_kallisto.sh
  • also available on many BRCF pods under /mnt/bioi/script.
    • many pre-built references also available in /mnt/bioi/ref_genome
  • email or come talk to me Anna if you have questions or problems

UCSC Genome Browser

• Main UCSC Genome Browser web site
• Beta Test browser site - most up-to-date datasets and features; can be buggy
• Visualize mapped data at UCSC genome browser on this wiki
• File formats - BED format especially is widely used
• Table browser - Browse and download data in different formats
• ENCODE data downloads at UCSC - useful for getting data to work with

Transcriptome-aware aligners

• HISAT2 – https://daehwankimlab.github.io/hisat2/
  
  • fast, with support for alignment to single and "population" of genomes
  • paper: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html
• STAR (Spliced Transcripts Alignment to a Reference) – ultra-fast RNA-seq aligner
  • releases: https://github.com/alexdobin/STAR/releases
  • paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/
  • STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
• TopHat - http://ccb.jhu.edu/software/tophat/index.shtml
  
  • exon-aware sequence alignment (uses bowtie2/bowtie )
• kallisto - https://pachterlab.github.io/kallisto/about
  • ultra-fast RNA-seq pseudoaligner that goes straight from FASTQ to estimated transcript abundances

Alignment analysis

• SAM (Sequence Alignment Map) format specification (SAM1.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
• samtools – by Heng Li
  • SAM/BAM conversion, flag filtering, sorting, indexing, duplicate filtering
  • older 0.1.xx versions: http://samtools.sourceforge.net/
  • newer 1.3+ versions: http://www.htslib.org/
• Picard toolkit – http://broadinstitute.github.io/picard/
  • SAM/BAM utilities that are read-group aware
  • especially MarkDuplicates for flagging duplicate alignments
    • http://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates
• bedtools – http://bedtools.readthedocs.org/en/latest/
  
  • All sub-commands: http://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html
  • Swiss army knife for all manner of common BED, BAM, VCF, GFF/GTF file manipulation.
  • See BEDTools Overview for some common use cases.
  • Available in the TACC module system
• RNA-seq QC, metrics & plotting tools:
  • RSeQC – http://rseqc.sourceforge.net/

  • RNA-SeQC (Broad Institute) –

    • https://software.broadinstitute.org/cancer/cga/rna-seqc
    • https://software.broadinstitute.org/cancer/cga/rnaseqc_run
  • RNA-QC-Chain – http://bioinfo.single-cell.cn/rna-qc-chain.html

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
• HTS format specifications – http://samtools.github.io/hts-specs/
  • clearinghouse page for a number of NGS formats (SAM, CRAM, VCF, BCF, etc.)
• 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
    • NCBI documentation
    • SRA toolkit downloads
• BioITeam script for converting GTF/GFF3 files to BED format
  • /work/projects/BioITeam/common/script/gtf_to_bed.pl
• UCSC file format conversion scripts - useful for getting to/from wig WIG and bed BED to corresponding binary formats.
  • Make sure you download the correct script scripts 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

...

• • Also available as a BioContainers module

UCSC Genome Browser

• Main UCSC Genome Browser web site
  • File formats - BED format especially is widely used
  • Table browser - Browse and download data in different formats
  • ENCODE data downloads at UCSC - useful for getting data to work with
  • Beta Test browser site - most up-to-date datasets and features; can be buggy

RNAseq/Transcriptome analysis

• General RNA-seq Differential Gene Expression (DGE) analysis workflow from R's Bioconductor:
  • https://www.bioconductor.org/help/workflows/rnaseqGene/
• Gene quantification from BAM/BED file reads
  • featureCounts (part of the Subread package) – http://subread.sourceforge.net/
  • HTSeq – https://htseq.readthedocs.io/en/master/
• HISAT2, StringTie, BallGown suite – https://ccb.jhu.edu/software/hisat2/index.shtml
  
  • transcriptome-aware alignment & quantification from the Johns Hopkins group who brought you the Tuxedo pipeline – but much faster!
  • paper: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html
• DESeq2 – R Bioconductor package for DGE
  
  • DESeq (version 1) documentation:
    • https://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
    • while DESeq2 is more sophisticated, reading the original documentation is a better introduction to concepts
  • DESeq2 documentation:
    • http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
• kallisto – https://pachterlab.github.io/kallisto/
  • RNA-seq pseudoaligner that goes straight from FASTQ to estimated transcript abundances
    
    • blindingly fast – but only to transcriptome
  • companion quantification tool is sleuth – http://pachterlab.github.io/sleuth/about
  • overview presentation – 2015-10-21-Kallisto.Anna.pdf
• The Tuxedo pipeline: RNAseq with tophat/cufflinks
  • one of the first tool suites for transcriptome-aware RNA-seq alignment and quantification
    • rarely used now, as other tools are much faster & more accurate
  • RNAseq analysis protocol article in Nature Protocols
  • tophat - TopHat- http://ccb.jhu.edu/software/tophat/index.shtml
    
    • exon-aware sequence alignment (uses bowtie2/bowtie )
    cufflinks - transcript assembly, differential expression & regulation
    • cufflinks resource bundles for selected organisms (gff GFF annotations, pre-built bowtie2 references, etc.)

Variant calling

• The 1000 Genomes project - catalog of human genetic variants
• Tools
  • Broad institute GATK - complex but powerful; used by cuffquant, cuffnorm, cufflinks – http://cole-trapnell-lab.github.io/cufflinks/manual/
    • transcript quantification, normalization, differential expression
• Dhivya Arasappan's Introduction to RNA Seq CBRS 2021 summer school course

Variant calling

• Broad institute GATK (Genome Analysis Tool Kit) – https://software.broadinstitute.org/gatk/documentation/
  
  • complex but powerful
  • used by TCGA (The Cancer Genome Atlas), 1000 Genomes
• File formats
  • VCF (Variant Call Format) v4.0 - initially developed by 1000 Genomes project
    • list of tools and format specs

...

• • MAF (Mutation Annotation Format) – developed by The Cancer Genome Atlas (TCGA)
• The International Genome Sample Resource – follow-on to the 1000 Genomes project 
  
  • catalog of human genetic variants
• Dan Deatherage's Genome Variant Analysis CBRS 2021 summer school course

Genome Annotation

• GO – http://geneontology.org/
  • The Gene Ontology resource, a large source of information on the functions of genes
• GOrilla – http://cbl-gorilla.cs.technion.ac.il/
  • Gene Ontology enRIchment anaLysis and visuaLizAtion tool
• GSEA – https://www.gsea-msigdb.org
  • Gene Set Enrichment Analysis
• DAVID – https://david.ncifcrf.gov/
  
  • Functional annotation from user-supplied gene lists
• GREAT – http://bejerano.stanford.edu/great/public/html/splash.php
  
  • Genomic Regions Enrichment of Annotations Tool
  • Takes bed files as input and outputs enriched genes, GO-terms, motifs, etc.
    • human, mouse, zebrafish
• MEME-suite – http://meme-suite.org/
  
  • A motif identification and discovery tool.  Works with most species.
  • Takes FASTA files as input
    • filter your BAM/BED files to get the regions of interest
    • then convert to FASTA using bedtools bamtofastq.