SOAP: short oligonucleotide alignment program

TY - JOUR

T1 - SOAP

T2 - short oligonucleotide alignment program

AU - Li, Ruiqiang

AU - Li, Yingrui

AU - Kristiansen, Karsten

AU - Wang, Jun

PY - 2008

Y1 - 2008

N2 - MOTIVATION: 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 multithreaded parallel computing, and has a batch module for multiple query sets. AVAILABILITY: http://soap.genomics.org.cn CONTACT: [email protected].

AB - MOTIVATION: 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 multithreaded parallel computing, and has a batch module for multiple query sets. AVAILABILITY: http://soap.genomics.org.cn CONTACT: [email protected].

U2 - 10.1093/bioinformatics/btn025

DO - 10.1093/bioinformatics/btn025

M3 - Journal article

C2 - 18227114

SN - 1367-4803

VL - 24

SP - 713

EP - 714

JO - Bioinformatics

JF - Bioinformatics

IS - 5

ER -