Please notice that this repository is outdated. The most updated version of SMIS can be found here: https://github.com/SangerHpag/smis.git
Scaffolding pipeline using data from long reads technologies (PacBio, ONT) to scaffold an initial draft assembly. The long reads are shred in smaller segments (f.i. 1000 bp) to create fake mate-pairs. The fake mates are then aligned against the draft assembly and the spinner scaffolder looks for links between contigs and creates scaffolds.
Original pipeline from Zemin Ning (zn1@sanger.ac.uk): http://www.sanger.ac.uk/science/tools/smis. Version here modified to use the bwa aligner instead of smalt, and to automize compiling and running.
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