subSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool subSeq

Tool usage distribution map

This map represents all the scientific publications referring to subSeq per scientific context
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subSeq specifications


Unique identifier OMICS_05533
Name subSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained Yes




No version available

Publication for subSeq

subSeq citations


Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet

PLoS One
PMCID: 5918799
PMID: 29694397
DOI: 10.1371/journal.pone.0195481

[…] Reads assigned to the species T. trichiura and T. muris and the Ascaris genus by the LCA algorithm, were extracted using seqtk version 1.0-r31 and the subseq command. Reads were re-mapped to the T. trichiura sequence from humans in Uganda (KT449826), the Ascaris sp. sequence from haplotype 07 (PUG3-1-H07) or the T. muris sequence (NC_028621) using b […]


Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil

BMC Microbiol
PMCID: 5879832
PMID: 29609542
DOI: 10.1186/s12866-018-1171-2

[…] ng phiX sequences were removed by mapping the reads to the phiX reference genome (Genbank acc. nr. J02482.1) using “BWA mem” with default settings []. Reads aligning were removed using seqtk with the subseq command []. Downstream processing and sequence analysis was performed using Mothur (v. 1.36.1) according to the Mothur Illumina MiSeq SOP []. Briefly, paired-end reads were joined using “make.c […]


Automated identification of multiple micro organisms from resequencing DNA microarrays

Nucleic Acids Res
PMCID: 1636417
PMID: 17012284
DOI: 10.1093/nar/gkl565

[…] ks: initial filtering of individual HybSeqs into SubSeqs suitable for sequence similarity comparisons (), database querying of individual SubSeqs () and taxonomic comparison of BLAST returns for each SubSeq (). The NCBI BLAST and taxonomy databases were used for the queries and images were obtained on February 7, 2006. For the ProSeq grouping Task(II), ProSeqs were compared to determine if they su […]

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subSeq institution(s)
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA
subSeq funding source(s)
This work was supported by NIH (R01 HG002913).

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