Strand NGS statistics

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Popular tool citations

chevron_left Gene set enrichment analysis Normalization Bioinformatics workflows Gene fusion detection Differential expression Data analysis Bioinformatics workflows Bioinformatics workflows Bioinformatics workflows Novel transcript quantification Alternative splicing events identification Bioinformatics workflows Bioinformatics workflows Variant detection chevron_right
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Protocols

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Strand NGS specifications

Information


Unique identifier OMICS_01120
Name Strand NGS
Alternative names Avadis NGS, Avadis
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS, Windows
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline Strand NGS Team <>

Strand NGS in pipelines

 (8)
2017
PMCID: 5730124
PMID: 29240787
DOI: 10.1371/journal.pone.0189102

[…] recommendations. the obtained cdna fragment libraries were sequenced on an illumina nextseq500 using default parameters (single read). all the bioinformatics were performed on the strand avadis ngs (v3.0) software (strand life sciences pvt.ltd). raw sequence quality was checked for gc content, base quality and composition using fastqc and strandngs. quality trimmed reads were aligned […]

2016
PMCID: 4751506
PMID: 26868178
DOI: 10.1038/srep21693

[…] in . alignment to the mouse genome (mm9) was performed using tophat (http://tophat.cbcb.umd.edu/). all aligned reads were exported in bam format, and subsequent data analysis was performed using avadis ngs (strand scientific intelligence, san francisco, ca, usa). rna expression analysis was performed at the exon level, and expression data were normalized with trimmed mean of m values (tmm). […]

2016
PMCID: 4786119
PMID: 26963095
DOI: 10.1371/journal.pone.0150582

[…] “sources”. the target genes of all smv-responsive dems were predicted following the `find targeted genes' step under the section `results interpretation' in the small rna analysis workflow using the strand ngs software (strand life sciences, version 2.1) and the web tool psrnatarget []. filtering based on expression changes and predicted targeting resulted in the genes that showed at least […]

2016
PMCID: 5056764
PMID: 27723829
DOI: 10.1371/journal.pone.0164250

[…] reads were mapped to a human genome reference sequence (hg19) using clc genomics workbench software (clc bio, aarhus, denmark), and the mapped data were exported as bam files and imported to strand ngs analysis software (agilent technologies). for downstream gene expression analysis, the expression level of genes was quantitated by counting the number of reads mapped to the genes. […]

2016
PMCID: 5415474
PMID: 27888582
DOI: 10.1111/jdi.12586

[…] using a sureselect kit (51 mb version 4; agilent technologies, santa clara, ca, usa), and sequenced using a hiseq 1000 sequencer (illumina, san diego, ca, usa). nucleotide alterations were called by avadis ngs 1.3.1 (dna chip research, yokohama, japan) or samtools 0.1.17 software (https://sourceforge.net/projects/samtools/files/samtools/). we searched for nucleotide alterations shared by cases 1 […]


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Strand NGS in publications

 (75)
PMCID: 5928069
PMID: 29712892
DOI: 10.1038/s41424-018-0015-6

[…] in the present study we analyzed ffpe specimens of patients with biliary dysplasia in the intraductal biopsy and cca in further clinical course by applying a targeted, cca-specific dual strand ngs-based analysis. thereby, 1.8 non-synonymous mutations per tumor and 2.3 non-synonymous mutations per biopsy were identified. this is consistent with an estimated amount of 2.1 mutations […]

PMCID: 5910417
PMID: 29679048
DOI: 10.1038/s41598-018-24782-5

[…] (n = 3 controls and 3 mutants) using rneasy miniprep kit (qiagen). illumina truseq rna-seq was performed, paired end 75 bp, with a minimum of 20 million reads per sample. data were analyzed using strand ngs software. bam files were generated using mouse build mm10. data was filtered on read quality metrics, including removal of reads aligning to more than one position in the genome, requiring […]

PMCID: 5805715
PMID: 29422531
DOI: 10.1038/s41598-018-21146-x

[…] hg19 build reference sequence by the life technologies ion torrent suite. the aligned bam files were used for further analyses. the bam files, separated by specific bar codes, were uploaded to the strand ngs software (san francisco, ca, usa). quality control was assessed by the strand ngs programme, which determined the pre- and post-alignment qualities of the reads per sample. the aligned […]

PMCID: 5839406
PMID: 29515775
DOI: 10.18632/oncotarget.23955

[…] cells; the fold differences and statistical significance were confirmed in both 143b and hela cells (table ). the identified genes were processed using the “pathway analysis” software package (strand ngs software version 2.0), and we focused on down-regulated and up-regulated pathways (table ). “notch signaling”, “transcriptional activity of smad2-3-4 heterotrimer” and “aryl hydrocarbon […]

PMCID: 5917777
PMID: 29301063
DOI: 10.1093/toxsci/kfx291

[…] from 0 ppm controls and the other from 100-ppm hcp-exposed group, were sequenced using a miseq sequencing system (illumina, inc., san diego, california), and then data analysis was performed using strand ngs (next-generation sequencing) analysis software (strand genomics, inc., san francisco, california). the genomic regions showing hypermethylation of cpg sites in the promoter region […]


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Strand NGS institution(s)
Strand Genomics, Inc, India

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