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Welcome to the BTEP bioinformatics tools selector guide. Scroll through this guide and click on the triangular tab next to each analysis category to identify software(s) that will help you accomplish your goals.

While many of the tools in these packages are powerful and can perform sophisticated analyses, people unfamiliar with bioinformatics analysis of complex data sets should consider consulting a bioinformatics analyst to ensure the validity of their methodology and conclusions.

Open Source Bioinformatics Tools

Note that this list of open source bioinformatics tools is not exhaustive because there are many open source tools that are available.

Biowulf applications

Unix applications for bioinformatics include those used for

  • Assessing next generation sequencing data quality
  • Quality and adapter trimming of next next generation sequencing data
  • Manipulation of alignment files
  • Variant calling
  • Differential gene expression analysis
  • Peak calling for ChIP sequencing

Many of these applications are installed on Biowulf. See here for the list of bioinformatics applications available through Biowulf.

See Biowulf High Performance Computing system for more information on getting started with Biowulf.

R

Data visualization
Data wrangling

R has an extensive collection of packages for bioinformatics that facilitate analysis of RNA, ChIP, and ATAC sequencing data. Many of these packages are housed under the Bioconductor repository. Outside of Bioconductor, there is Seurat, a popular tool for single cell RNA sequencing.

Python

Data visualization
Data wrangling

Python has packages such as Scanpy, scVelo,and scDeepCluster that facilitate single cell RNA sequencing analysis.

Commercial Bioinformatics Packages

Molecular Biology

Sequence comparison

Phylogenetics

  • CLC Genomics Workbench
    • What data types can I start my analysis with?
      • Sequence alignment result
  • Geneious Prime
    • What data types can I start my analysis with?
      • Sequence alignment result
  • Lasergene
    • What data types can I start my analysis with?
      • Sequence alignment result

Molecular cloning

  • CLC Genomics Workbench
    • What file types can I start my analysis with?
      • FASTA
      • Genbank
  • Geneious Prime
    • What file types can I start my analysis with?
      • Genbank
      • .DNA
      • FASTA
  • Lasergene
    • What file types can I start my analysis with?
      • .DNA
      • FASTA
      • Genbank
  • SnapGene
    • What file types can I start my analysis with?
      • Genbank
      • .DNA

Restriction digest

  • CLC Genomics Workbench
    • What file types can I start my analysis with?
      • .DNA
      • FASTA
      • Genbank
  • Geneious Prime
    • What file types can I start my analysis with?
      • .DNA
      • FASTA
      • Genbak
  • Lasergene
    • What file types can I start my analysis with?
      • FASTA
      • Genbank
      • SEQ
  • SnapGene
    • What file types can I start my analysis with?
      • .DNA
      • FASTA
      • Genbank

Ligation simulation

PCR primer design

  • CLC Genomics Workbench
    • What file types can I start my analysis with?
      • FASTA
      • Genbank
  • Geneious Prime
    • What file types can I start my analysis with?
      • FASTA
      • Genbank
  • Lasergene
    • What file types can I start my analysis with?
      • FASTA
      • Genbank
  • SnapGene
    • What file types can I start my analysis with?
      • FASTA
      • Genbank

CRISPR editing

Variant Analysis

Single nucleotide variants

  • CLC Genomics Workbench (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
  • Geneious Prime (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
  • Partek Flow (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
      • BAM

Insertions, deletions

  • CLC Genomics Workbench (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
  • Geneious Prime (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
  • Partek Flow (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
      • BAM
      • VCF

Structural variants

Low frequency variants

Copy number analysis

  • CLC Genomics Workbench (sequencing based)
    • The copy number detection tools in CLC Genomics Workbench are designed to analyze targeted sequencing data. Users can input FASTQ or BAM to perform copy number analysis using the CNV detection tool. If starting with FASTQ, users will need to align using the built-in aligner.
    • CLC Genomics Workbench uses a proprietary algorithm for CNV analysis. Refer to the white paper for details.
    • What file types can I start my analysis with?
      • FASTQ
      • BAM
  • Partek Genomics Suite (array based)
    • What file types can I start my analysis with?
      • Affymetrix CEL
      • Affymetrix Axiom Summary File
      • Agilent
      • Illumina GenomeStudio
      • Illumina Final Report text file
      • NimbleGen Pair or CGH Data summary files

Loss of heterozygosity

  • Partek Genomics Suite (array based)
    • What file types can I start my analysis with?
      • Affymetrix CHP
      • Affymetrix Gentoyping Text
      • Illumina GenomeStudio
      • Illumina Final Report Text

Association analysis

  • Partek Genomics Suite (array based)
    • What file types can I start my analysis with?
      • Affymetrix CHP
      • Affymetrix Genotyping Text
      • Illumina GenomeStudio
      • Illumina Final Report Text

Trio analysis

  • Partek Genomics Suite (array based)
    • What file types can I start my analysis with?
      • Affymetrix CHP
      • Affymetrix Genotyping Text
      • Illumina GenomeStudio
      • Illumina Final Report Text

Promoter tiling array

  • Partek Genomics Suite (array based)
    • What file types can I start my analysis with?
      • Affymetrix CEL
      • Affymetrix Data
      • NimblGen Pair Files
      • Text

Gene Expression

Gene expression by microarray

  • CLC Genomics Workbench
    • What file types can I start my analysis with?
      • Affymetrix Gene Chip (CHP, NetAFFx, CEL)
      • Illumina BeadChip
      • TSV
      • CSV
  • Partek Flow
    • What file types can I start my analysis with?
      • Affymetrix CEL
      • Illumina BeadChip IDAT
      • TSV of Illumina GenomeStudio output
  • Partek Genomics Suite
    • What file types can I start my analysis with?
      • Affymetrix CELL
      • Agilent TXT
      • Illumina GenomeStudio
      • Applied Biosystems TaqMan RQ Manager files
      • SOLiD SAGE output
      • NanoString CSV
      • Fluidigm

microRNA by microarray

  • Partek Genomics Suite
    • What file types can I start my analysis with?
      • Affymetrix CEL
      • Applied Biosystems TaqMan RQ manager files
      • Illumina GenomeStudio
      • SOLiD SAGE output files
      • GenePix (GPR) files
      • ImaGene (Exiqon) files
      • AB Small RNA Count files
      • Agilent data
      • NanoString output files
      • Fluidigm output files
      • TXT
  • Qlucore Omics Explorer
    • What file types can I start my analysis with?
      • Affymetrix CEL
      • Affymetrix CHP
      • Agilent TEXT
      • TXT, TSV, CSV

RNA sequencing

microRNA sequencing

Single cell RNA sequencing

  • Partek Flow
    • What file types can I start my analysis with?
      • BCL
      • FASTQ
      • BAM
      • Count tables
      • barcodes.tsv, features.tsv, counts.mtx
      • h5
      • Seurat object
  • Qlucore Omics Explorer
    • What file types can I start my analysis with?
      • 10x single cell data

Spatial transcriptomics

  • Partek Flow (implements Space Ranger to analyze 10x Visium Spatial Gene Expression data)
    • What file types can I start my analysis with?
      • FASTQ (sequences) and JPEG/TIFF for spatial images

Epigenetics

ATAC sequencing

  • Partek Flow
    • What file types can I start my analysis with?
      • FASTQ
      • BAM

Single cell ATAC sequencing

  • Partek Flow
    • What file types can I start my analysis with?

ChIP sequencing

Methylation array

  • Partek Genomics Suite
    • What file types can I start my analysis with?
      • Illumina GenomeStudio output
      • Illumina Infinium methylation 450/850 IDAT files

Methylation tiling array

  • Partek Genomics Suite
    • What file types can I start my analysis with?
      • Illumina Infinium methylation 450/850 IDAT files
      • Affymetrix CEL files
      • Agilent
      • NimbleGen Pair files
      • TXT

Bisulfite sequencing

Metagenomics

Metagenomics

  • Geneious Prime (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ
  • Partek Flow (sequencing based)
    • What file types can I start my analysis with?
      • FASTQ

Biological Insights

Pathway, network, and gene ontology

  • Partek Flow
    • What file types can I start my analysis with?
      • FASTQ
      • BAM
      • TXT
  • Partek Genomics Suite
    • What file types can I start my analysis with?
      • BAM
      • TXT
  • Qiagen Ingenuity Pathway Analysis
    • What file types can I start my analysis with?
      • TSV, CSV, or EXCEL file that contain gene, differential expression, and p-values
      • TSV, CSV, or EXCEL containing genetic gain or loss of function information
  • Qlucore Omics Explorer
    • What file types can I start my analysis with?
      • BAM
      • CSV