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Soap

swMATH ID: 8915
Software Authors: Ruiqiang Li; Yingrui Li; Karsten Kristiansen; Jun Wang
Description: 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.
Homepage: http://soap.genomics.org.cn/
Related Software: BWA; Samtools; BLAT; R; SSAHA; PatternHunter; SHRiMP; STAR; ZOOM; TopHat; BLAST; PSI-BLAST; BEDTools; MUSCLE; DIALIGN; MAFFT; Bowtie 2; Velvet; GATK; HTSeq
Cited in: 26 Publications

Standard Articles

1 Publication describing the Software Year
SOAP2: an improved ultrafast tool for short read alignment
Li, Ruiqiang; Yu, Chang; Li, Yingrui; Lam, Tak Wah; Yiu, Siu-Ming; Kristiansen, Karsten; Wang, Jun
2009
all top 5

Cited by 84 Authors

3 Iliopoulos, Costas S.
3 Pissis, Solon P.
2 Barton, Carl
2 Daykin, Jacqueline W.
2 Gog, Simon
2 Kärkkäinen, Juha
2 Mäkinen, Veli
2 Mouchard, Laurent
2 Välimäki, Niko
1 Athitsos, Vassilis
1 Attolini, Camille Stephan-Otto
1 Bonizzoni, Paola
1 Boucher, Christina
1 Carugo, Oliviero
1 Chen, Yangjun
1 Cox, Anthony J.
1 Das, Gautam Kumar
1 Daugelaite, Jurate
1 Davis, Sean L.
1 de Ridder, Corne
1 Della Vedova, Gianluca
1 Eisenhaber, Frank
1 Flouri, Tomáš
1 Gagie, Travis
1 Giancarlo, Raffaele
1 Gîrdea, Marta
1 Groult, Richard
1 Guesnet, Yannick
1 Jakobi, Tobias
1 Ji, Yuan
1 Karhu, Kalle
1 Keith, Jonathan M.
1 Kempa, Dominik
1 Kotsifakos, Alexios
1 Kourie, Derrick G.
1 Kroiss, Manuel
1 Kucherov, Gregory
1 Kuhnle, Alan
1 Ladra, Susana
1 Langmead, Ben
1 Lecroq, Thierry
1 Lee, Inbok
1 Lefebvre, Arnaud
1 Léonard, Martine
1 Liang, Han
1 Liang, Shoudan
1 Lin, Jimmy
1 Liu, Yongchao
1 Manzini, Giovanni
1 Mathé, Ewy
1 Mun, Taher
1 Musombuka, Themba K.
1 Noé, Laurent
1 Norris, Clift jun.
1 O’Driscoll, Aisling
1 Papapetrou, Panagiotis
1 Park, Kunsoo
1 Petri, Matthias
1 Pirola, Yuri
1 Policriti, Alberto
1 Previtali, Marco
1 Prieur-Gaston, Élise
1 Puglisi, Simon J.
1 Rizzi, Raffaella
1 Rosone, Giovanna
1 Rossell, David
1 Scaturro, Davide
1 Schmidt, Bertil
1 Schulz-Trieglaff, Ole B.
1 Shen, Carol
1 Shen, Tony
1 Shomroni, Orr
1 Sleator, Roy D.
1 Stefan, Alexandra
1 Stöcker, Almond
1 Tomescu, Alexandru Ioan
1 Tsui, Kam-Wah
1 Utro, Filippo
1 Vezzi, Francesco
1 Wolff, Alexander
1 Wu, Yujia
1 Xu, Yanxun
1 Yuan, Yuan
1 Zhang, Qiong

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