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

doi:10.1093/bioinformatics/btp336

Cited by 3,224 publications

(2,373 citation statements)

References 5 publications

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“…Data from deep-sequencing analyses of total (-ribosomal RNA) RNA, polyA + enriched mRNA and ribosome foot-printing were collected and the resulting sequences were aligned using the following method: the linker sequences at the 3′ ends were removed prior to alignment using SOAP2.20, allowing a maximum of two total mismatches (Li et al, 2009). Ribosome footprint reads were assigned to a specific A-site nucleotide by an offset of +15 from 5′ end of the read (only for ribosome foot-printing data set).…”

Section: Methodsmentioning

confidence: 99%

The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

Kimmig

Diaz

Zheng

et al. 2012

eLife

126

157

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The unfolded protein response (UPR) monitors the protein folding capacity of the endoplasmic reticulum (ER). In all organisms analyzed to date, the UPR drives transcriptional programs that allow cells to cope with ER stress. The non-conventional splicing of Hac1 (yeasts) and XBP1 (metazoans) mRNA, encoding orthologous UPR transcription activators, is conserved and dependent on Ire1, an ER membrane-resident kinase/endoribonuclease. We found that the fission yeast Schizosaccharomyces pombe lacks both a Hac1/XBP1 ortholog and a UPR-dependent-transcriptional-program. Instead, Ire1 initiates the selective decay of a subset of ER-localized-mRNAs that is required to survive ER stress. We identified Bip1 mRNA, encoding a major ER-chaperone, as the sole mRNA cleaved upon Ire1 activation that escapes decay. Instead, truncation of its 3′ UTR, including loss of its polyA tail, stabilized Bip1 mRNA, resulting in increased Bip1 translation. Thus, S. pombe uses a universally conserved stress-sensing machinery in novel ways to maintain homeostasis in the ER.DOI: http://dx.doi.org/10.7554/eLife.00048.001

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Section: Methodsmentioning

confidence: 99%

The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

Kimmig

Diaz

Zheng

et al. 2012

eLife

126

157

View full text Add to dashboard Cite

show abstract

“…The two major alignment algorithms used are hash table–based algorithms (BLAST, MAQ[68], Eland[59]) and Burrows Wheeler transform (BWT)-based methods (SOAP2[69], BWA[70], Bowtie[71]). Hash table-based algorithms use an indexing scheme that enables ultra-fast searches for short sequences of a defined length k (k-mer matches or seeds) with up to m mismatches.…”

Section: Massively Parallel Sequencingmentioning

confidence: 99%

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

Gundry

Vijg

2012

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

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DNA mutations are the source of genetic variation within populations. The majority of mutations with observable effects are deleterious. In humans mutations in the germ line can cause genetic disease. In somatic cells multiple rounds of mutations and selection lead to cancer. The study of genetic variation has progressed rapidly since the completion of the draft sequence of the human genome. Recent advances in sequencing technology, most importantly the introduction of massively parallel sequencing (MPS), have resulted in more than a hundred-fold reduction in the time and cost required for sequencing nucleic acids. These improvements have greatly expanded the use of sequencing as a practical tool for mutation analysis. While in the past the high cost of sequencing limited mutation analysis to selectable markers or small forward mutation targets assumed to be representative for the genome overall, current platforms allow whole genome sequencing for less than $5,000. This has already given rise to direct estimates of germline mutation rates in multiple organisms including humans by comparing whole genome sequences between parents and offspring. Here we present a brief history of the field of mutation research, with a focus on classical tools for the measurement of mutation rates. We then review MPS, how it is currently applied and the new insight into human and animal mutation frequencies and spectra that has been obtained from whole genome sequencing. While great progress has been made, we note that the single most important limitation of current MPS approaches for mutation analysis is the inability to address low-abundance mutations that turn somatic tissues into mosaics of cells. Such mutations are at the basis of intra-tumor heterogeneity, with important implications for clinical diagnosis, and could also contribute to somatic diseases other than cancer, including aging. Some possible approaches to gain access to low-abundance mutations are discussed, with a brief overview of new sequencing platforms that are currently waiting in the wings to advance this exploding field even further.

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“…We compared Ψ-RA with Bowtie [5] and SOAP2 [21], as the two successful representatives of BWT genre, and with PerM [6] and mrsFast [8], which are based on spaced seeds and ordinary q- grams respectively. The index sizes of those aligners are 2.3GB (Bowtie), 6.1GB (SOAP2), 12.4GB (PerM), and 19.5GB (mrsFast).…”

Section: Resultsmentioning

confidence: 99%

Ψ-RA: a parallel sparse index for genomic read alignment

Külekçi¹,

Hon

Shah

et al. 2011

BMC Genomics

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BackgroundGenomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same species share the majority of their genomes, short reads alignment provides an alternative and much more efficient way to sequence the genome of a particular individual than does direct sequencing. Among many strategies proposed for this alignment process, indexing the reference genome and short read searching over the index is a dominant technique. Our goal is to design a space-efficient indexing structure with fast searching capability to catch the massive short reads produced by the next generation high-throughput DNA sequencing technology.ResultsWe concentrate on indexing DNA sequences via sparse suffix arrays (SSAs) and propose a new short read aligner named Ψ-RA (PSI-RA: parallel sparse index read aligner). The motivation in using SSAs is the ability to trade memory against time. It is possible to fine tune the space consumption of the index based on the available memory of the machine and the minimum length of the arriving pattern queries. Although SSAs have been studied before for exact matching of short reads, an elegant way of approximate matching capability was missing. We provide this by defining the rightmost mismatch criteria that prioritize the errors towards the end of the reads, where errors are more probable. Ψ-RA supports any number of mismatches in aligning reads. We give comparisons with some of the well-known short read aligners, and show that indexing a genome with SSA is a good alternative to the Burrows-Wheeler transform or seed-based solutions.ConclusionsΨ-RA is expected to serve as a valuable tool in the alignment of short reads generated by the next generation high-throughput sequencing technology. Ψ-RA is very fast in exact matching and also supports rightmost approximate matching. The SSA structure that Ψ-RA is built on naturally incorporates the modern multicore architecture and thus further speed-up can be gained. All the information, including the source code of Ψ-RA, can be downloaded at: http://www.busillis.com/o_kulekci/PSIRA.zip.

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SOAP2: an improved ultrafast tool for short read alignment

Cited by 3,224 publications

References 5 publications

The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

Ψ-RA: a parallel sparse index for genomic read alignment

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