Difference between SSPACE and AlignGraph

Question

[Ric]

Hi, I read this article ( http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/ ) and they used first SSPACE and then AlignGraph. Is SSPACE and AlignGraph not the same or would it be enough just to use AlignGraph?

Thank you in advance.

Mic

[natasha.sernova]

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

http://bioinformatics.oxfordjournals.org/content/30/12/i319.full

"In our performance tests, AlignGraph was able to substantially improve the contigs and scaffolds from several assemblers. For instance, 28.7–62.3% of the contigs of Arabidopsis thaliana and human could be extended, resulting in improvements of common assembly metrics, such as an increase of the N50 of the extendable contigs by 89.9–94.5% and 80.3–165.8%, respectively. In another test, AlignGraph was able to improve the assembly of a published genome (Arabidopsis strain Landsberg) by increasing the N50 of its extendable scaffolds by 86.6%. These results demonstrate AlignGraph’s efficiency in improving genome assemblies by taking advantage of closely related references".

Scaffolding pre-assembled contigs using SSPACE

http://bioinformatics.oxfordjournals.org/content/27/4/578.long

"“We developed the SSPACE (SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension) program to scaffold pre-assemblies produced by any desired assembly tool. The input is given by a set of contig sequences and Illumina paired-read files. The user can specify whether the paired reads are used only for scaffolding or also for contig extension. We compared our method to the Abyss scaffolder on a bacterial (Escherichia coli) and fungal (Grosmannia clavigera). Both methods significantly reduce the number of contigs in a comparable manner, although SSPACE achieves overall better results. To prove the suitability of SSPACE also on large eukaryotic genomes, we tested its performance against SOAP on the giant panda genome assembly. We show that SSPACE is a valuable tool for scaffolding pre-assembled contigs.”"

Answer 1

[Chris Fields]

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.