Frequently Asked Questions

Tutorial Questions

Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?

Question: Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?

In our experience, when both long and short reads are allowed as input, the difference comes down to the order in which set is assembled first. For example, Unicycler assembles the short reads first (which can be good, because they are more accurate), and then scaffolds these into larger contigs using long reads. Other tools (or workflows) often assemble long reads first (which can also be good because these can span repeat regions), then correct this assembly with information from the more accurate short reads. There may also be other variations on long/short read assembly, and/or iterations of these types of steps (assemble, correct). My preference is to assemble long reads first, but that’s because I’m really interested in covering repeat regions. If accuracy was the aim, rather than contig length, the short-reads-first approach may be better. For even more complexity … I think some tools now allow input of “trusted contigs” - i.e. contigs assembled from other tools. Ryan Wick has a new tool called Trycyler that can take in multiple assemblies to make a consensus (bacterial genomes).

Igv

Add Mapped reads track to IGV from Galaxy

Tip: Add Mapped reads track to IGV from Galaxy

1. Install IGV (if not already installed)
2. Launch IGV on your computer
3. Check if the reference genome is available on the IGV instance
4. Expand the BAM dataset with the mapped reads in the history
5. Click on the local in display with IGV to load the reads into the IGV browser

6. Switch to the IGV instance

   The mapped reads track should appear. Be sure that all files have the same genome ID

Add genome and annotations to IGV from Galaxy

Tip: Add genome and annotations to IGV from Galaxy

1. Upload a FASTA file with the reference genome and a GFF3 file with its annotation in the history (if not already there)
2. Install IGV (if not already installed)
3. Launch IGV on your computer
4. Expand the FASTA dataset with the genome in the history
5. Click on the local in display with IGV to load the genome into the IGV browser
6. Wait until all Dataset status are ok

7. Close the window

   An alert ERROR Parameter "file" is required may appear. Ignore it.

8. Expand the GFF3 dataset with the annotations of the genome in the history
9. Click on the local in display with IGV to load the annotation into the IGV browser

10. Switch to the IGV instance

    The annotation track should appear. Be careful that all files have the same genome ID

Visualisation

Using IGV with Galaxy

Tip: Using IGV with Galaxy

You can send data from your Galaxy history to IGV for viewing as follows:

1. Install IGV on your computer (IGV download page)
2. Start IGV
3. In recent versions of IGV, you will have to enable the port:
   • In IGV, go to View > Preferences > Advanced
   • Check the box Enable Port
4. In Galaxy, expand the dataset you would like to view in IGV
   • Make sure you have set a reference genome/database correctly (dbkey) (instructions)
   • Under display in IGV, click on local

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