Scaffolding pre-assembled contigs using SSPACE

Bioinform., 2011

1,210 citations recorded by the source corpus.

Citations in the corpus

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information (2014, methodology): “Optionally the user may also provide scaffold sequences generated with dedicated software ( e.g. SSPACE [5] or SOPRA [4]).”
Toward almost closed genomes with GapFiller (2012, background): “Even though the distance information of pairedread sequences can help to bridge these difficult areas by linking the contigs into larger scaffolds [4,5], scaffolding does not solve the inherent problem of low-coverage and repetitive elements: it does not add novel sequence information to the draft a”
An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “Finally, in stage 5 the broken-up scaffolds are rescaffolded using SSPACE [9].”
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads (2012, background): “For example, scaffolding is one of the key steps in whole-genome sequencing, in which paired read mappings are used to estimate the order and intervening distance between initial contiguous sequences (contigs) [9].”
MeDuSa: a multi-draft based scaffolder (2015, methodology): “0 (Boetzer et al., 2011), RAGOUT V. 1.0 (Kolmogorov et al., 2014). The first four of these scaffolders are paired ends-based and the choice to use these specific ones was based on both their performances and their usability as assessed by Hunt et al. (2014). The choice to use the recently developed ”