An isogroup is a collection of contigs containing reads that imply connections between them. A discussion of the assembly process (see Section 1.1) explains how breaks can be introduced into the multiple alignments of overlapping reads, leading to branching structures between them. After attempting to resolve the branching structures, the Transcriptome Assembler groups all contigs whose branches could not be resolved into collections called isogroups. Using rules described in the following section, the assembler traverses the various paths through the contigs in an isogroup to produce the set of isotigs that gets reported. All possible paths through the contigs in an isogroup are traversed unless one or more thresholds is reached (see Section 5.2.2).

An isotig is meant to be analogous to an individual transcript. Different isotigs from a given isogroup can be inferred splice-variants. The reported isotigs are the putative transcripts that can be constructed using overlapping reads provided as input to the assembler. Connections between contigs in an isogroup are represented by sequences (reads) that have alignments diverging consistently towards two or more different contigs (see Figure 103) or by a depth spike (Section 5.2.2.2). Traversal from the start contig to the end contig or from the end contig to the start contig should yield the same but reverse-complemented isotig sequence.