3.0 years ago by
University of Illinois Urbana-Champaign
Pretty simple difference: SSPACE is a tool that takes a genome assembly and uses Illumina reads (typically mate-pair but can also be paired-end) to join (e.g. scaffold) them into longer sequences/scaffolds, using the joins found by aligning the reads to scaffolds. So, in this case sequences are scaffolded using Illumina mate pairs as evidence. No additional inferences are made.
AlignGraph, on the other hand, uses alignment of both the scaffolds and paired-end reads against a close reference genome to infer joins. In this case the evidence includes alignments to the reference. The use of a reference genome in this case is helped by using the paired-end reads as additional supportive evidence for the joins.
There are a few other tools that use some variations on this latter approach: RACA and Ragout2.