Scaffolding with scaff10x:
1 Barcoded tags are extracted from 10Xg raw sequencing reads and appended to read names for further processing
2 The reads are mapped to the draft assembly using either BWA or SMALT
3 Barcodes are sorted together with contigs as well as mapping coordinates
4 A relation matrix is built to record the shared barcodes among the contigs which may be linked
5 Order and orientation of linked contigs are determined after nearest neighbours are found.
Breaking scaffolds (or contigs) with break10x:
Steps 1, 2 and 3 are the same as for scaff10x
4 The barcode depth is monitored for each scaffold, if this is reduced by more than 15% with respect to the scaffold average barcode depth, the point of minimum depth is considered to be an assembly error and the scaffold is broken at that point. Exception are points close to long N-gaps unless the N-Gaps was added by scaff10x.
5 The location of breaking points are printed out in a file and the broken scaffolds are printed in a fasta file