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Galaxy: Comparison of NGS Analysis Platforms at USC

Partek Flow

Pre-alignment QA/QC

  • QA/QC plots
  • Reads and adapter trimming

Aligners

  • Bowtie/Bowtie2
  • BWA
  • STAR
  • TopHat/TopHat2
  • GSNAP
  • Isaac2

RNA-seq

  • Partek E/M quantification
  • Gene-Specific Analysis (limma-based differential expression analysis)
  • ANOVA
  • Cufflinks-Cuffdiff

DNA-seq

  • Partek genotype likelihood
  • Samtools
  • FreeBayes
  • LoFreq
  • Strelka
  • CNVkit

ChIP-seq

  • MACS2

Visualization

  • 3-D PCA
  • t-SNE
  • Hierarchical clustering
  • Volcano plot

CLC Genomics Workbench

Aligners/Assembler

  • CLC sequence aligner
  • CLC genome assembler
  • MetaGeneMark

DNA-seq

  • CLC variant caller
  • CLC structural variant caller

Bisulfite-seq

  • CLC bisulfite sequence aligner

miRNA-seq

  • Align to reference genome
  • Direct-count toward mirBase miRNAs

Meta-genomics

  • 16s/18s OTU clustering
  • Metagenome assembly
  • Microbial community analysis
  • Metagenome functional analysis
  • Burst plot

Molecular biology tools

  • Primer design
  • Sequence retrieval

Galaxy (Local and Docker)

FASTQ QA/QC

  • FASTQC

BAM QA/QC

  • DeepTools

ChIP-seq

  • MACS2
  • diffBind (differential binding)
  • CEAS (annotation)
  • Ngs.plot (visualization)

RNA-seq

  • DESeq2
  • EdgeR
  • HISAT2
  • StringTie
  • Sailfish
  • featureCount

Variant analysis

  • SnpEff
  • SnpSift
  • VCFtools

NGS utility tools

  • BEDtools
  • BAMtools
  • Picard
  • SAMtools

Text and general molecular biology utility tools

  • File format converters
  • Sequence retrieval
  • Operate on Genomic Intervals
  • EMBOSS Molecular Biology Tools