Phusion2 Files

# smis_pipeline: an assembly pipeline to improve scaffolds using Oxford Nanopore or PacBio long reads
# Long reads are shreded into small segments (1000bp or 2000bp) to make fake mate pairs
# Genome scaffolder spinner is used for scaffolding
# Say if you have an existing assembly from Illumina reads target.fasta
# and ONT long reads: ontreads.fastq

Usage: 

./smis_pipeline -nodes 20 -score 50 -len 2000 -step 200 -contig 3000 -edge 5 <ONT_fasta/q_file> <assembly_fasta/q_file> <scaffold-output.fasta_file>
       nodes - number of CPUs requested
       score - minimum smith-waterman alignment score to report a hit
       len - length of fregments of fake mate pairs
       step - jump length to cut out fregments
       contig - minimum contig length to be included for scaffolding
       edge - minimum number of edges to confirm a merge

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Install: 
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gunzip smis.tar.gz 
tar xvf smis.tar 
make

Note: You need to type the full path in order to make it work.


Please contact Zemin Ning ( zn1@sanger.ac.uk ) for any further information.