Strand NGS protocols

Strand NGS specifications

Information


Unique identifier OMICS_01120
Name Strand NGS
Alternative name Avadis NGS
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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Maintainer


  • person_outline Strand NGS Team <>

Strand NGS IN pipelines

 (2)
2017
PMCID: 5483006
PMID: 28331057
DOI: 10.1242/dmm.028555

[…] were mapped or aligned to the mouse genome using tophat2 version 2.0.9 aligner against the ucsc reference sequence database (mm10). gene expression data, mapped and filtered, was quantitated using strand ngs 2.0. normalization of read count values was applied using the deseq package. at least 100 raw reads in all samples was the cut-off threshold for consideration in the analysis. […]

2013
PMCID: 3590643
PMID: 23471139
DOI: 10.3389/fphys.2013.00039

[…] were downloaded from vectorbase1. output fastq illumina files were mapped to the reference genome with tophat (trapnell et al., 2009). resulting sequence alignment files were uploaded into the avadis ngs software (strand scientific intelligence, ca, usa), where quantification and normalization were carried out. prior to quantification using the deseq normalization method, the read list […]

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

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