Bioinformatics Software: Galaxy

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

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

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