Basic tool for scaffolding of pre-assembled contigs
Advanced tool for scaffolding of pre-assembled contigs
Tool to close gaps within scaffolds
BaseClear Genome Browser
In addition to NGS-services for the sequencing itself, BaseClear also offers bioinformatics services. Our bioinformatics specialists offer you exactly what you need, based on CLCbio software in combination with other state-of-the-art methods..
SSPACE basic
SSPACE is a stand-alone program for scaffolding pre-assembled contigs using paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (FASTA or FASTQ). The final scaffolds are provided in FASTA format.
SSPACE has shown excellent performance on various datasets. The results have been published in the high-impact journal Bioinformatics (2011, vol. 27(4), pag. 578-9), but the method is also frequently cited in other papers.
ALGORITHM SSPACE basic
SSPACE basic v1.0 is the original version that was released after publication. The algorithm is a modified version of the SSAKE protocol (Warren et al., 2007) and further improved as described in Boetzer et al., 2011). It works as follows:
