Workflows
What is a Workflow?Filters
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 ...
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 ...
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 ...
A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses
GermlineShortV_biovalidation
Type: Shell Script
Creators: Georgina Samaha, Tracy Chew, Cali Willet, Nandan Deshpande
Submitter: Georgina Samaha
Objective. Biomarkers have become important for the prognosis and diagnosis of various diseases. High-throughput methods such as RNA-sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia, a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes, limitations in diagnosis and ...
ESCALIBUR
Escalibur Population Genomic Analysis Pipeline is able to explore key aspects centering the population genetics of organisms, and automates three key bioinformatic components in population genomic analysis using Workflow Definition Language (WDL: https://openwdl.org/), and customised R, Perl, Python and Unix shell scripts. Associated programs are packaged into a platform independent singularity image, for which the definition file is provided.
The workflow for analysis using Escalibur ...
CWL based workflow to assemble haploid/diploid eukaryote genomes of non-model organisms
The workflow is designed to use both PacBio long-reads and Illumina short-reads. The workflow first extracts, corrects, trims and decontaminates the long reads. Decontaminated trimmed reads are then used to assemble the genome and raw reads are used to polish it. Next, Illumina reads are cleaned and used to further polish the resultant assembly. Finally, the polished assembly is masked using inferred repeats ...
Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
Based on the official pmx tutorial.
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial. ...