SOAP: short oligonucleotide alignment program. We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets.
Keywords for this software
References in zbMATH (referenced in 7 articles )
Showing results 1 to 7 of 7.
- Shomroni, Orr: Development of algorithms and next-generation sequencing data workflows for the analysis of gene regulatory networks (2017)
- Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
- Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)
- Daugelaite, Jurate; O’Driscoll, Aisling; Sleator, Roy D.: An overview of multiple sequence alignments and cloud computing in bioinformatics (2013)
- Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq: A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes (2012) ioport
- Zhang, Michael Q.; Smith, Andrew D.: Challenges in understanding genome-wide DNA methylation (2009) ioport
- Li, Ruiqiang; Li, Yingrui; Kristiansen, Karsten; Wang, Jun: SOAP: Short oligonucleotide alignment program. (2008) ioport