SOAP2.21
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SOAPaligner/soap2 is a program for faster and efficient alignment for short oligonucleotide onto reference sequences. SOAPaligner/soap2 is compatible with numerous applications, including single-read or pair-end resequencing.
Quick Start
- To use SOAP2, import your data in fastq format.
- Resources: http://soap.genomics.org.cn/index.html
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> soap2_aligner_paired_end_illumina |
Input File(s)
Use 10K_SRR192294_1.fastq and 10K_SRR194494_2.fastq from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Use these parameters within the DE app interface:
- Reference genome: Arabidopsis lyrata (Ensembl 14)
- Minimum insert size allowed for PE alignment: 400
- Maximum insert size allowed for PE alignment: 600
- Leave all other parameters as defaults.
Output File(s)
Expect four files as output. For the test case, the output files you will find in the example_data directory are named 10K_SRR192294_1.fastq_10K_SRR192294_2.fastq.soap2, 10K_SRR192294_1.fastq.unmapped.fa, 10K_SRR192294_1.fastq.unpaired.soap2 and soap_output.sam.
Tool Source for App
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