Avadis NGS

Application data
Biological application domain(s)	ChIP-Seq, DNA-Seq, RNA-Seq, Small RNA, Pathway Analysis
Principal bioinformatics method(s)	Alignment, Quality Control, Sequence Analysis, Visualization, Biological Contextualization
Technology	Illumina, 454, ABI SOLiD, Ion Torrent, PacBio
Created at	Strand Scientific Intelligence
Maintained?	Yes
Input format(s)	SAM, BAM, BED, ELAND, FASTA, FASTQ
Software features	Rich Visualization, Identify effects of SNPs on transcripts, Identify Structural Variants from Paired Reads (Insertions, Deletions, Translocations, Inversions), Identify binding site peaks in ChIP-Seq data, Identify motifs around binding sites, Determine gene expression levels and identify differentially expressed genes De-convolve transcript expression levels and identify differential splice variants, Identify Novel Exons, Identify Novel Splice Junctions, Identify Fusion Genes Perform QC on Reads, determine on-and off-target reads, and filter anomalous reads, Determine Enriched GO Terms, Determine Significant Pathways
Programming language(s)	Java, R
Licence	Commercial
Operating system(s)	Windows, Linux, Mac OS X

Summary: Avadis NGS is a desktop software platform for alignment, analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. It supports workflows for RNA-Seq, DNA-Seq, and ChIP-Seq analysis and is designed with the biologist in mind. 200px|right

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Description

Avadis® is the data mining and visualization platform at the core of all bioinformatics products developed by Strand. The platform has been integrated with state-of-the-art algorithms for alignment, quality control, analysis and management of next-generation sequencing data on a wide range of computing infrastructures.

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• Avadis NGS Homepage [ edit link ]

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