Workflows
What is a Workflow?Filters
Analysis of variation within individual COVID-19 samples using Illumina Single End data. More info can be found at https://covid19.galaxyproject.org/genomics/
Type: Galaxy
Creator: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
Submitter: Bert Droesbeke
Download
Tests Analysis of variation within individual COVID-19 samples using Illumina Paired End data. More info can be found at https://covid19.galaxyproject.org/genomics/
Type: Galaxy
Creator: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
Submitter: Bert Droesbeke
Dating the most recent common ancestor (MRCA) of SARS-CoV-2. The workflow is used to extract full length sequences of SARS-CoV-2, tidy up their names in FASTA files, produce a multiple sequences alignment and compute a maximum likelihood tree. More info can be found at https://covid19.galaxyproject.org/genomics/
Type: Galaxy
Creator: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
Submitter: Bert Droesbeke
This workflow uses Illumina and Oxford Nanopore reads that were pre-processed to remove human-derived sequences. Two assembly tools are used: spades and unicycler. In addition to assemblies (actual sequences) the two tools produce assembly graphs that can be used for visualization of assembly with bandage. More info can be found at https://covid19.galaxyproject.org/genomics/
Type: Galaxy
Creator: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
Submitter: Bert Droesbeke
Preprocessing of raw SARS-CoV-2 reads. This workflow contains an alternate starting point to avoid the data to be downloaded from the NCBI SRA. More info can be found at https://covid19.galaxyproject.org/genomics/
Type: Galaxy
Creator: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
Submitter: Bert Droesbeke
Preprocessing of raw SARS-CoV-2 reads. More info can be found at https://covid19.galaxyproject.org/genomics/
Type: Galaxy
Creator: Dannon Baker, Marius van den Beek, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Bert Droesbeke, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Delphine Larivière, Gildas Le Corguillé, Andrew Lonie, Nicholas Keener, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
Submitter: Bert Droesbeke
