SOAP2: an improved ultrafast tool for short read alignment

By Ruiqiang Li, Chang Yu, Yingrui Li, T. T. Lam, Siu Ming Yiu, Karsten Kristiansen, Jun Wang. Bioinform., 2009

3,707 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ec9b42dafc20aaf6b0e470226459e9a374105654

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

1. Heng Li
2. Mark J. P. Chaisson
3. S. Cloutier
4. Santosh Kumar
5. Travis W. Banks
6. Alicia Oshlack
7. Glenn Tesler
8. Erik P. Garrison

In Genetics

1. Anders Albrechtsen
2. Thorfinn Sand Korneliussen
3. Heng Li
4. Mark J. P. Chaisson
5. Rasmus Nielsen
6. Glenn Tesler
7. Alicia Oshlack
8. Erik P. Garrison

In Molecular Biology

1. Steven L. Salzberg
2. Heng Li
3. Alicia Oshlack
4. Mark D. Robinson
5. Glenn Tesler
6. Mark J. P. Chaisson
7. Matthew D. Young
8. Nils Homer

Citations in the corpus

• Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, neutral): “Mapping/alignment BWA [48] Bowtie [49] Novoalign [50] SOAP [51] MrFAST [52] CloudBurst [53] BFAST [54] MUMer [26] MOSAIK http://bioinformatics.”
• Computational methods for transcriptome annotation and quantification using RNA-seq (2011, methodology): “Seed methods Short-read mapping package (SHRiMP) 41 Smith-Waterman extension Aligning reads to a reference transcriptome”
• Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. (2011, methodology): “Mappers that use the Burrows-Wheeler transform (BWA [Li and Durbin 2009], SOAP2 [Li et al. 2009], Bowtie [Langmead et al. 2009]) are very fast but tend to be less sensitive than are the best hash-based mappers.”
• A survey of sequence alignment algorithms for next-generation sequencing (2010, methodology): “Finding inexact matches with a suffix/prefix trie Of published aligners that can be used for queryreference alignment, MUMmer [42] and OASIS [45] are based on suffix tree, Vmatch [38] and Segemehl [46] on enhanced suffix array, and Bowtie [47], BWA [48], SOAP2 [49], BWT-SW [50] and BWA-SW [51] on FM”
• Faster and More Accurate Sequence Alignment with SNAP (2011, methodology): “BWT-based aligners, including Bowtie, SOAP2, BWA, and BWA-SW [6, 10, 7, 8], align reads against a prefix trie of the reference genome, which is represented compactly using the Burrows-Wheeler transform [4].”
• Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study (2011, background): “SOAPdenovo [8], ABySS [9], and VelvetOases (hereafter referred as Oases) [10] were reported to be successfully applied to transcriptome assembly of various organisms [3,9,11-13].”
• Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients (2015, methodology): “The sequenced reads were then aligned to the non–repeat-masked human reference genome (National Center for Biotechnology Information build 37/hg19) using the Short Oligonucleotide Alignment Program 2 (SOAP2) (49).”
• Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates (2012, methodology): “, respectively. Paired-end read mapping was performed with SOAP v2.20”