SeqMan NGen® is DNASTAR's software for performing next-gen sequence assembly using Illumina, Roche 454, Ion Torrent, PacBio, and Sanger data. ArrayStar can use SeqMan NGen assemblies as input. Some common workflows involve using SeqMan NGen to:
•Create a transcriptome/RNA-Seq assembly using RPK, RPM or RPKM normalization, then import it into ArrayStar for downstream analysis.
•Create an assembly then open it in ArrayStar’s SNP Table to compare large sets of SNPs and affected genes.
•Create an assembly to import into ArrayStar for Validation Control Accuracy testing. This workflow is described in Validation Control Accuracy.
•Create a specialized RNA-Seq assembly using Bioconductor-based DESeq2 or edgeR packages, then view the results of those analyses in ArrayStar’s Gene and Isoform tables and use them to filter for differentially-expressed genes of interest.