SeqAlto specifications


Unique identifier OMICS_09276
Name SeqAlto
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Wing Hung Wong <>

Publication for SeqAlto

SeqAlto in publications

PMCID: 5073887
PMID: 27766935
DOI: 10.1186/s12859-016-1216-1

[…] {r}$\end{document}r to the reference genome, we considered several popular aligners: bowtie2 [], bwa-sw [], cushaw2 [], smalt [], srmapper [], shrimp2 [], razers [], gassst [], seqalto [], masai [], and soap2 []. most aligners employed a seed-and-extend strategy, which first finds exact matches (seeds) between reads and the genome, and then extend such seeds to full […]

PMCID: 4674900
PMID: 26678826
DOI: 10.1186/1471-2105-16-S17-S3

[…] inappropriately affected the true complexity of the genomes., we selected 10 popular short-read aligners that employ different algorithmic techniques and indexing structures: shrimp2 [], mrfast [], seqalto [], gassst [], bowtie2 [], bwa-sw [], soap2 [], cushaw2 [], masai [], and smalt []., we used default parameters to run these programs because these aligners appeared to perform well […]

PMCID: 4625105
DOI: 10.1186/1471-2105-16-S15-P17

[…] of genome complexity and, respectively, alignment accuracy and chromosomal coverage. the result was validated using 9 state-of-the-art aligners (bowtie2[], bwa-sw[], cushaw2, masai[], mrfast, seqalto, shrimp2[], smalt, and soap2[]) and two different data sets. the first dataset, which consists of 100 genomic sequences including bacteria, plants and eukaryotes, was used to correlate […]

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SeqAlto institution(s)
Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; Bina Technologies Inc., Redwood City; Department of Statistics, Stanford University, Stanford, CA, USA

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