The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').
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The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.
Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to firstname.lastname@example.org. Thank you.
Rationale and background:
This app can be used to convert SAM file to Sorted BAM file which is generally needed for downstream bioinformatics tools.
- A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
- Input file(s)
- Input file Name: SAM files generated from any mapper
- Output File name: Name of the output file (output.sorted.bam is default)
The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/Samtools-SAMtoSortedBAM
- Input file: BowtieOutput.sam
- Output: Default file name (BowtieOutput.sorted)
Successful execution of the QUAST assessment pipeline will create the following files and folders: