Using SOAP2 to perform short read alignment

Peter Li (GigaScience) and Huayan Gao (Chinese University of Hong Kong)

The latest version of BGI's short read alignment tool is SOAP2. It is an order of magnitude faster compared to SOAP1 and also now supports a wide range of read lengths compared to its predecessor.

Input data

An example dataset of short reads is available for testing SOAP2:

Workflow

These 2 datasets are fed into the SOAP2 alignment mapping tool:

Tool execution

SOAP2 is available from the list of tools on the left hand side:

In contrast to SOAP1, SOAP2 uses index files for aligning reads to a reference sequence. To use the paired reads example data set, the hs_chr22_extract index files should be used, and the forward and reverse inputs configured as above. The remaining parameters can be left to their default values.

Results

When the SOAP2 process is executed, the job will run and the following results containing a file of alignments and a file of non-alignments should appear: