SysCall protocols

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SysCall specifications

Information


Unique identifier OMICS_01080
Name SysCall
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Lior Pachter <>

Publication for SysCall

SysCall in pipeline

2012
PMCID: 3409179
PMID: 22859977
DOI: 10.1371/journal.pone.0041356

[…] and sequence context. this data set is typically either from a part of the data set being “recalibrated” (genome analysis toolkit, or gatk) or from a separate data set with special characteristics (syscall). here, we combine the advantages of these approaches by adding synthetic rna spike-in standards to human rna, and use gatk to recalibrate base quality scores with reads mapped […]


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SysCall in publications

 (5)
PMCID: 5952957
PMID: 29718213
DOI: 10.1093/gigascience/giy023

[…] -t has no effect with -c}\\ \hbox{[main] executing /bin/bash /scif/apps/main/scif/runscript}\\ \hbox{ hello world!}\\ \hbox{\% time\qquad seconds\qquad usecs/call\qquad calls\qquad errors syscall}\\ \hbox{----------------}\quad \hbox{----------------}\quad \hbox{----------------}\quad \hbox{----------------}\quad \hbox{----------------}\\ \qquad\hbox{----------------}\\ […]

PMCID: 4870477
PMID: 27330913
DOI: 10.1186/s40064-016-2257-7

[…] decade (jiang et al. ; srivastava and giffn ; nance et al. ). however, the precondition of vmi’s functioning is the security of hypervisor, where vmi tools are deployed., just like system calls (syscall, for short) may be used by attackers to escalate privileges, hypercalls can be used by attackers to break virtualization’s isolation and escape virtual machines’ constraints and finally […]

PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] over a read (a special feature of ccs) and the mean quality value into an error probability., finally, three tools use more refined error models that are worth a more detailed look: the authors of syscall [] first analysed error occurrences and identified a new type of systematic error when using illumina platforms. these errors show: (a) a drop in coverage compared with surrounding bases, (b) […]

PMCID: 4487316
PMID: 26401432
DOI: 10.6028/jres.118.012

[…] may not have been controlled is instruction reordering at the cpu (micro-op) level causing instructions to effectively move into or out of the timed region. the linux kernel implementation of the syscall that clock_gettime invokes retrieves values that are traceable to the time stamp counter via the process scheduler. although steps are taken in the code to stabilize the results, the authors […]

PMCID: 3409179
PMID: 22859977
DOI: 10.1371/journal.pone.0041356

[…] batch effects in a run-specific manner, compensating for them requires training data sets. the two previously proposed approaches either use a separate data set with special characteristics (e.g., syscall uses overlapping paired-end reads ) or use the data set itself excluding regions known to have variants (e.g., genome analysis toolkit, or gatk, base quality score recalibration ). here, […]


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SysCall institution(s)
Department of Mathematics, University of California, Berkeley, Berkeley, CA, USA; Children's Hospital Oakland Research Institute, Oakland, CA, USA; Computer Science Division, University of California, Berkeley, Berkeley, CA; USA; Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA

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