Avadis NGS
Application data |
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Biological application domain(s) | ChIP-Seq, DNA-Seq, RNA-Seq, Small RNA, Pathway Analysis |
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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) | Mac, Windows, Linux |
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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