Creating contigs from 454 data
This tutorial covers the process of assembling 454 reads using afterParty.
**NOTE: afterParty uses the MIRA assembler with default parameters, which may not give the best assembly for your data. We recommend that you only use this method for "first pass" annotation or testing. For final assembly, we recommend running an assembler of your choice locally, then following the tutorial here. **
To create an assembly for your 454 data, first create a study. Point your browser to the AfterParty instance you are using (e.g. afterparty.bio.ed.ac.uk) and click login. Enter your username and password on the login page and click the login button.
Click my studies on the navigation bar at the top of the page and select add new.
AfterParty will create a new study and display a green message at the top of the screen informing you of this fact. To dismiss the message, click the x at the right. When you are logged in, and looking at one of your own studies, you can edit the names and descriptions of most things. You will see a pencil icon next to things that you can edit. To edit the study name, just click on it and you'll get a text entry box. Type the new name (e.g. "my first study") and hit the save button.
###Create a compound sample and an assembly
In AfterParty, all assemblies (and by extension, contigs) belong to a compound sample. This usually represents a species. To create a new compound sample, click the **add new compound sample" button.
You'll be taken to the compound sample page and get a green message as before. Just like with the study you created, you can edit the name of the compound sample by clicking on it. Change the name to reflect your source organism.
Follow the same procedure to add a Sample, an Experiment, and a Run.
From the run page, click the trimmed reads tab and select your fastq file, then click upload reads. Depending on the speed of your network, this may take a while. Once the upload is complete, return to the run page and the trimmed reads tab and click the assemble reads button. Wait for the assembly process to finish, then reload the Compound Sample page and you'll see the new assembly listed. Clicking on the new assembly will take you to the assembly page.
You'll probably now want to generate some annotations for the contigs.
###Add BLAST annotation
To add BLAST annotation to your contigs, click the generate BLAST annotation button on the Generate annotation tab.
You'll be taken to the list of running jobs again, but this time it will take quite a bit longer. The progress column tells you how many contigs have been BLASTed and how long you will have to wait.
For the sample dataset, this should only be a few minutes, so wait until the job is finished, then go back to the assembly page. You will notice that the contig table looks a little bit more interesting. Some of the contigs (but not all!) have entries in the annotation column.
If you click on the contig name in the first column (with the eye symbol) you will be taken to the overview page for that contig and see where the BLAST hits are.
You can also type in the search box at the top right of the table to filter the contigs by annotation. Try typing "mitochondrial".
###Add interproscan annotation
To add InterProScan annotation to your contigs, just click the generate InterProScan annotation button.
You'll probably have to wait a bit longer than you did for the BLASTs. Once the job is finished, go back and reload the assembly page. You'll see quite a lot more in the annotation column.
