SeqAn protocols

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SeqAn specifications

Information


Unique identifier OMICS_14825
Name SeqAn
Alternative name seqan2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 2.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andreas Döring <>

Publications for SeqAn

SeqAn in pipeline

2017
PMCID: 5333174
PMID: 28251872
DOI: 10.1186/s12862-016-0870-2

[…] developed by the authors was used here to apply filtering rules to the raw vcf and to format contigs for the phylogenetic software). all indel positions were realigned using the code from the seqan [] library and then excluded. generally, we kept snp positions near indels, except for the regions with high probability of containing strs (for this, we measured the “dimeric” entropy value […]


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SeqAn in publications

 (27)
PMCID: 5891031
PMID: 29590103
DOI: 10.1371/journal.pgen.1007267

[…] dcs blocks across all genomes along with an estimate of their ancestral order at the time of the polyploidy., step 1: homology search. for at-α, we used a fast homology search program based on the seqan package [, ] to identify pairs of homologous genes, one from a genome with at-α and one from c. violacea. we defined a pair of genes as being homologous for the purposes of dcs inference […]

PMCID: 5826272
PMID: 29451494
DOI: 10.7554/eLife.32942.030

[…] which is a second from-scratch implementation of the same functionality to minimize software bugs. the scientific data libraries numpy and scipy (), pandas (), xarray (), seqan () and its derivative seqanpy (https://github.com/iosonofabio/seqanpy) were used for number crunching. matplotlib () and seaborn () were used for plotting. the gene expression and virus counts […]

PMCID: 5740500
PMID: 29242366
DOI: 10.15252/msb.20177728

[…] show conserved patterns and were therefore not used here for verification., binding windows for competing intron rna secondary structures were predicted for all candidate clusters of mxes using the seqan package (döring et al, ). the identified binding windows of all homologous genes were aligned using muscle (edgar, ) and the rna secondary structures predicted by rnaalifold (viennarna package) […]

PMCID: 5500889
PMID: 28675155
DOI: 10.1038/ncomms15737

[…] from the samples were sequenced together on one lane in paired-end mode, with a read length of 50 bases., fastq files for six embryo timepoints were adaptor trimmed using flexbar (https://github.com/seqan/flexbar): flexbar -r read1.fastq -p read2.fastq -f i1.8 –a [adaptor sequences file] --pre-trim-phred 30 -n 20 -s –t [timepoint suffix]; and demultiplexed using pybarcodefilter.py […]

PMCID: 5465553
PMID: 28595639
DOI: 10.1186/s40168-017-0274-6

[…] the accuracy of using read mapping to infer function improves considerably when using 200 base pair reads relative to using 100 base pair reads but increases much more slowly thereafter. using the seqan library [], we searched for translated reads that, after smith-waterman local alignment [], matched database sequences at a) two identical seven residue “words,” b) >80% amino acid identity […]


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SeqAn institution(s)
Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany; imec, Belgium; Intel Corporation (UK) Limited, UK
SeqAn funding source(s)
Supported by the Intel® Parallel Compute Center at FU Berlin.

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