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Protocols

DNAnexus specifications

Information


Unique identifier OMICS_01217
Name DNAnexus
Software type Framework/Library
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/DNAnexus

Versioning


No version available

Maintainer


  • person_outline Dnexus Team

Additional information


https://wiki.dnanexus.com/Home

DNAnexus citations

 (138)
library_books

Inactivation of the tight junction gene CLDN11 by aberrant hypermethylation modulates tubulins polymerization and promotes cell migration in nasopharyngeal carcinoma

2018
PMCID: 5946489
PMID: 29747653
DOI: 10.1186/s13046-018-0754-y

[…] data were expressed as fold-enrichment of normalized experiment tags over normalized background tags within regions and compared by false discovery rate adjusted p value (q value) and analyzed by the DNAnexus platform (DNAnexus, CA, USA). For NPC microarray analysis, gene expression in 9 NPC tumor was compared with that of “one-combined non-tumors” by using the one-way analysis of variance (ANOVA) […]

call_split

Conditional mouse models support the role of SLC39A14 (ZIP14) in Hyperostosis Cranialis Interna and in bone homeostasis

2018
PLoS Genet
PMCID: 5903675
PMID: 29621230
DOI: 10.1371/journal.pgen.1007321
call_split See protocol

[…] ocedures.Exome sequencing was performed on a female patient using the NimbleGen SeqCap EZ Human Exome V2 enrichment panel on the HiSeq2000 (Illumina Inc.). Data analysis was performed with DNA Nexus (DNAnexus Inc.; dnanexus.com). Variants were filtered for their absence in dbSNP and non-coding and synonymous variants were excluded. As published previously, we already defined a linkage region on ch […]

call_split

Combining targeted panel based resequencing and copy number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies

2018
Sci Rep
PMCID: 5869593
PMID: 29588463
DOI: 10.1038/s41598-018-23520-1
call_split See protocol

[…] A specific custom pipeline for Illumina Nextera technology implemented on the commercial DNAnexus platform (https://www.dnanexus.com/) was used for the bioinformatics analysis as previously described,. Briefly, Prinseq-lite v0.20.3 was used to calculate read statistics, and BWA-MEM v0.7.5 […]

library_books

Single molecule, full length transcript sequencing provides insight into the extreme metabolism of the ruby throated hummingbird Archilochus colubris

2018
GigaScience
PMCID: 5869288
PMID: 29618047
DOI: 10.1093/gigascience/giy009

[…] We performed initial data processing using SMRTanalysis 3.1 Iso-Seq pipeline using a DNANexus interface. From 40 SMRTcells, we produced 440.75 Gb of raw data, which was classified into 3.4 Gb of non-chimeric circular consensus (CCS) reads. CCS reads comprised 1.23M full-length, 1.27M […]

library_books

Stem Loop RNA Hairpins in Giant Viruses: Invading rRNA Like Repeats and a Template Free RNA

2018
Front Microbiol
PMCID: 5799277
PMID: 29449833
DOI: 10.3389/fmicb.2018.00101

[…] Mimivirus' transcriptome [data from (Legendre et al., ), available at: http://sra.dnanexus.com/studies/SRP001690/experiments] includes numerous short RNAs that are not homologous to Mimivirus' genome. Here we focus on a 42-nucleotide-long sequence (5′-GAGACACGCAACAGGGGATAGGCAAGGCAC […]

library_books

Hypermanganesemia due to mutations in SLC39A14: further insights into Mn deposition in the central nervous system

2018
Orphanet J Rare Dis
PMCID: 5791243
PMID: 29382362
DOI: 10.1186/s13023-018-0758-x

[…] o manufacturer’s protocol using HaloPlex technology. Sequencing was carried out on MiSeq sequencer (Illumina, San Diego, CA, USA). Data processing, variant calling and variant annotation were done by DNAnexus platform and Variant Studio software. The average of mean-coverage in the sample gene panel was 95% for a read depth of 20X. Filtering was performed by minor allele frequency < 1% and possibl […]

Citations

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DNAnexus institution(s)
DNAnexus, Mountain View, CA,USA; DNAnexus, San Francisco, CA, USA

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