Workflows

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245 Workflows visible to you, out of a total of 260

workflow-denovo-stacks

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • population map in text format

Steps and outputs

ustacks:

  • input reads go to ustacks.
  • ustacks assembles the reads into matching ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-ref-guided-stacks

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • population map in text format
  • reference genome in fasta format

Steps and outputs

BWA MEM 2:

  • The reads are mapped to the ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-qc-of-radseq-reads

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, in a collection
  • two adapter sequences in fasta format, for input into cutadapt

Steps and outputs

The workflow can be modified to suit your own parameters.

The workflow steps are:

  • Run ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

Work-in-progress

A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses

Type: KNIME

Creator: Julian Uszkoreit

Submitter: Julian Uszkoreit

Stable

Workflow for Illumina paired read quality control, trimming and filtering. Multiple paired datasets will be merged into single paired dataset. Summary:

  • FastQC on raw data files
  • fastp for read quality trimming
  • BBduk for phiX and (optional) rRNA filtering
  • Kraken2 for taxonomic classification of reads (optional)
  • BBmap for (contamination) filtering using given references (optional)
  • FastQC on filtered (merged) data

All tool CWL files and other workflows can be found here: Tools: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Stable

StructuralVariants Workflow

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Daniel López-López

Submitter: Laura Rodriguez-Navas

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