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Protocols

DuffyNGS specifications

Information


Unique identifier OMICS_17846
Name DuffyNGS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Version 1.4.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bob Morrison <>

DuffyNGS citations

 (2)
call_split

Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose

2017
PMCID: 5760070
PMID: 29281637
DOI: 10.1371/journal.pgen.1007131
call_split See protocol

[…] was done using illumina nextseq with libraries generated using the nebnext directional library kit (neb). alignment to the h37rv genome was done using bowtie 2.0 [], read depth was determined using duffyngs tools (available at https://github.com/sturkarslan/duffyngs), and visualized using arraystar (dnastar)., for isolation of trehalose from wt m. marinum cells were grown in 7h9 containing 0.2% […]

library_books

Cyclic GMP Balance Is Critical for Malaria Parasite Transmission from the Mosquito to the Mammalian Host

2015
PMCID: 4453516
PMID: 25784701
DOI: 10.1128/mBio.02330-14

[…] from the same number of sporozoites for each line. equal volumes of extract from wt and pdeγ− sporozoites were used to assay for cgmp., raw fastq read data were processed using in-house r package duffyngs as originally described (). briefly, raw reads pass through a 3-stage alignment pipeline: (i) a prealignment stage to filter out unwanted transcripts, such as rrna, mitochondrial rna, […]


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