SAM_to_Sorted_BAM-0.1.9

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Rationale and background:

This app can be used to convert SAM file to Sorted BAM file which is generally needed for downstream bioinformatics tools.

Pre-Requisites

A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
Input file(s)
1. Input file Name: SAM files generated from any mapper
Output
1. Output File name: Name of the output file (output.sorted.bam is default)

Test/sample data

The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/Samtools-SAMtoSortedBAM

Test run

Input file: BowtieOutput.sam
Output: Default file name (BowtieOutput.sorted)

Test Results

Successful execution of the QUAST assessment pipeline will create the following files and folders:

logs
BowtieOutput.sorted
BowtieOutput.sorted.bam.bai