SOAP2 Aligner
SOAP2 Aligner 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 Aligner, upload your data in FASTQ format. If you are using the single-end version of SOAP2 Aligner, you need only one input file. If you are using the paired-end version, you will need both Run 1 and Run 2 FASTQ files.
- Resources: http://soap.genomics.org.cn/soapaligner.html
Test Data
Input File(s)
Use 10K_SRR192294_1.fastq from http://mirrors.iplantcollaborative.org/example_data/soap2_aligner_paired_end_illumina_reads/10K_SRR192294_1.fastq alone for single-end SOAP2. Add 10K_SRR192294_2.fastq http://mirrors.iplantcollaborative.org/example_data/soap2_aligner_paired_end_illumina_reads/10K_SRR192294_2.fastq for paired-end SOAP2. as test data. Import from URL to get the data into your Discovery Environment account.
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
- Select a reference genome from the list - Brachypodium distachyon (line Bd21) v1
- All other parameters remain in their default state
Output File(s)
Expect a SOAP file and a SAM file as outputs.
- Single-end SOAP2
- Paired-end SOAP2
Tool Source for App
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