SeekDeep protocols

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SeekDeep specifications

Information


Unique identifier OMICS_24666
Name SeekDeep
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Javascript, Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.5.1
Stability Stable
Requirements
g++ or clang++ compiler
Maintained Yes

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Maintainers


  • person_outline Jeffrey Bailey <>
  • person_outline Nick Hathaway <>
  • person_outline Nick Hathaway <>

Additional information


http://baileylab.umassmed.edu/SeekDeep/multiplexTutorial_cmds.html

Publication for SeekDeep

SeekDeep in pipelines

 (2)
2018
PMCID: 5920075
PMID: 29700348
DOI: 10.1038/s41598-018-24585-8

[…] school of medicine., forward and reverse reads were merged using flash, trimmed for quality (sliding window = 50-bp, step size = 5-bp, quality threshold = 20) and collapsed by haplotype using seekdeep’s default illumina settings and allowing for one high quality mismatch within individuals. samples included in the final analysis were supported by high read coverage, with an average […]

2017
PMCID: 5732508
PMID: 29246158
DOI: 10.1186/s12936-017-2137-9

[…] torrent pgm platform (life technologies) at the university of north carolina chapel hill microbiome core facility. deep sequence data extraction, processing, and analyses were performed using the seekdeep targeted amplicon bioinformatics pipeline [–]. a workflow diagram is provided to outline the methods and provide additional details (additional file )., in order to compare ama1 amino acid […]


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SeekDeep in publications

 (6)
PMCID: 5932820
PMID: 29720181
DOI: 10.1186/s12936-018-2337-y

[…] samples were pooled and sequenced on the illumina hiseq 2500 (384-well plate with dual indexing, uci genomics high-throughput facility)., haplotypes of pvmsp1 and pfmsp1 variants were determined by seekdeep software developed by bailey lab at university of massachusetts amherst (http://baileylab.umassmed.edu/seekdeep). this software uses a clustering method to construct the most likely […]

PMCID: 5920075
PMID: 29700348
DOI: 10.1038/s41598-018-24585-8

[…] school of medicine., forward and reverse reads were merged using flash, trimmed for quality (sliding window = 50-bp, step size = 5-bp, quality threshold = 20) and collapsed by haplotype using seekdeep’s default illumina settings and allowing for one high quality mismatch within individuals. samples included in the final analysis were supported by high read coverage, with an average […]

PMCID: 5914063
PMID: 29685152
DOI: 10.1186/s12936-018-2322-5

[…] haplotypes. recently, multiple packages have been developed for de novo clustering of haplotypes from this type of data allowing detection of low frequency variants, such as haplotypr [] and seekdeep []., several studies have evaluated long amplicon deep sequencing to examine multiplicity of infection by sequencing mixtures of multiple lab strains. for example, patel et al. performed […]

PMCID: 5782373
PMID: 29361940
DOI: 10.1186/s12936-018-2193-9

[…] at the university of north carolina high throughput sequencing facility.table 1 , the paired-end sequences were stitched by flash [], and haplotype determination was performed using the program seekdeep [] using a quality cut-off of q30 > 0.75. in brief, sequence reads were first demultiplexed according to mids into amplicon-specific data, resulting in two independent amplicon reads sets […]

PMCID: 5732508
PMID: 29246158
DOI: 10.1186/s12936-017-2137-9

[…] torrent pgm platform (life technologies) at the university of north carolina chapel hill microbiome core facility. deep sequence data extraction, processing, and analyses were performed using the seekdeep targeted amplicon bioinformatics pipeline [–]. a workflow diagram is provided to outline the methods and provide additional details (additional file )., in order to compare ama1 amino acid […]


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SeekDeep institution(s)
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina School of Medicine, Chapel Hill, NC, USA; Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, NC, USA; Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
SeekDeep funding source(s)
Supported by NIH [5 R01 AI099473] (in part), 5 R01 AI089819]; NIH training [GM007092 and AI109979].

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