Avadis NGS supports the following data file formats:

• SAM (*.sam)
• BAM (*.bam)
• BED (*.bed)
• ELAND (*.txt, Illumina output format)
• GZIP (*.gz)

If you are about to send your data for sequencing you can request your sequencing facility to deliver the data in one of these formats.

If you already have your data and it is not in one of these formats there are free online tools available to convert your files.

Yes, you can. Version 1.3 of Avadis NGS includes our new aligner for small RNA, DNA-Seq, and ChIP-Seq data, called COBWeb. COBWeb is designed to handle both short reads and long reads, as well as allow an arbitrary number of gaps and mismatches. Watch this video to learn more about alignment in Avadis NGS and how COBWeb compares to other available alignment tools.

Data loading times vary depending on the hardware specifications of the computer you are using. As an example, Avadis NGS takes about 3 hours to import 150M reads. You can look up more examples and guidelines on loading, storage, and computation requirements here.

In RNA-Seq experiments, the key difference, compared to other software, is that Avadis NGS performs an extra step during import to ensure correct handling of multiply mapping reads. Based on the publication by Mortazavi et. al. at - http://www.nature.com/nmeth/journal/v5/n7/abs/nmeth.1226.html, the best way to handle multiply mapping reads is to distribute them to the genes that they map to in proportion to the number of uniquely mapping reads in those genes. This requires extra processing of the samples when they are imported and hence the comparatively longer import times.

Avadis NGS supports these three major NGS experiment workflows:

• RNA-Seq (transcriptome analysis) to detect:
  
  • SNPs/MNPs and small InDels, as well as predict their effects on transcripts
  • differential expression and splicing
  • novel genes and splice junctions
  • fusion genes

  
  

• DNA-Seq (whole genome and exome) to detect:
  
  • SNPs/MNPs and small InDels, as well as predict their effects on transcripts
  • large structural rearrangements, including insertions, deletions, inversions, as well as inter- and intra-chromosomal translocations

  
  

• ChIP-Seq (transcription regulation) to identify:
  • transcription factor binding sites using the PICS and MACS peak detection algorithms
  • motifs in the identified peak regions
  • translate identified regions into genes, that are good candidates for transcription factor regulation

  
  

In addition, Avadis NGS contains tools for quality control and filtering your reads by base quality, mapping score, alignment status and alignment score. Once you’ve completed your analysis, you can also perform tertiary analysis steps, like GO Analysis, GSEA, or pathway analysis to gain insight into the biological context of your analysis results.

We are working on implementing analysis support for miRNA-Seq, which will become available in a future release.

Register here to receive the latest updates on Avadis NGS!

The trial period lasts 20 days.

If you need more time, avadisngs [dot] sales [at] strandsi [dot] com (just ask)! We will work with you to help you determine if Avadis NGS is the right software solution for you.

We have plenty of online media to help you learn about Avadis NGS and keep abreast of updates to the software:

• Find out more about some of the great features of Avadis NGS in our Features section.
• Attend one of our live webinars and ask questions.
• Watch video tutorials to learn how specific features work.
• avadisngs [dot] sales [at] strandsi [dot] com (Request a private demo) of the software. You can even send us some of your own data and we'll show you how your data is visualized!
• Read the user guides online, or the user manual that comes with the software.

And if you have any questions, our technical support team is available around the clock during the business week. We always like to hear from you!

Our licensing models are explained here.

In a nutshell, you can choose to license in one, two, or three year chunks of time. For larger organizations, we also offer shared license and workgroup licensing options. avadisngs [dot] sales [at] strandsi [dot] com (Contact us) to find out more.