Tripal Galaxy Workflows

Galaxy Workflows

Only registered users can submit workflows. Please register an account.

This tool is in beta. If you find bugs or have problems, we'd appreciate hearing from you!

Quality Control - Perform trimming on raw next generation sequencing reads (Illumina only) with Trimmomatic and get a quality report from FastQC.

• Sequence quality control (single-end)
• Sequence quality control (paired-end)

Sequence Analysis

• Mapping - Map short next generation sequencing reads to a reference genome.

  • Short Read Mapping using Bowtie2 (single-end)
  • Short Read Mapping using Bowtie2 (paired-end)
  • Short Read Mapping using HISAT2 (single-end) (available soon)
  • Short Read Mapping using HISAT2 (paired-end) (available soon)

• Functional Gene Annotation - Get predicted function of gene sequences.

  • BLASTP to compare protein sequences to a protein database - SwissProt protein database provided, or upload your own protein database.
  • InterProScan protein domain functional analysis for protein or nucleotide sequences.

Transcriptomics

• RNA-Seq differential expression analysis (htseq-count, DESeq2)

  • Counting mapped reads
  • Differential expression analysis with DESeq2

Variant Analysis

• Short Variant Analysis with FreeBayes and SnpEff