Grouper

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis. Grouper is a tool for clustering and annotating contigs from de novo transcriptome assemblies. There are two main modules in Grouper: the clustering module and the labeling module. The former is based on the tool, RapClust, and is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. It relies on the fragment equivalence classes, orphaned read mappings and quantification information computed by these tools in order to determine how contigs in the assembly are potentially related and cluster them accordingly. The labeling module in Grouper is able to incorporate information from annotated genomes of closely related species to annotate contigs in the de novo assembly. Hence, the different modules of Grouper are able to efficiently utilize information from multiple sources to accurately cluster and annotate contigs from transcriptome assemblies.

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  1. Sahlin, Kristoffer; Medvedev, Paul: \textitDenovo clustering of long-read transcriptome data using a greedy, quality-value based algorithm (2019)