Phusion2 Files

# replace: genome assembly merge/replacement using cross-assembly alignment
# Say two assemblies have been produced using different algorithms: SOAP or Fermi
# The SOAP has long and reliable scaffolds, but lack of base accuracy at local contigs
# Fermi has almost no scaffolding and short contigs; but it has the highest base accuracy
# at contig level. 

# The pipeline of replace does this job by merging Fermi assembly with SOAP assembly
# The scaffold structure remains the same for the merged assembly, but contig sequences
# are replaced with Fermi contigs (high base accuracy). Also a lot of gaps may be closed
# as two assemblies were from different algorithms.

# Here we use Fermi assembly as ref assembly and SOAP as target assembly

Usage:

./replace -nodes 20 -score 300 <ref_fasta/q_file> <assembly_fasta/q_file> <merged.fasta_file>

./replace -nodes 20 -score 100 ref_fasta target_fasta merged.fasta

node:  number of CPU threads
score: Smith-waterman score

========
Install:
========
gunzip replace.tar.gz
tar xvf replace.tar
make

* note: you need to change the path in the python file multiNali.py 

cd replace-bin
vi multiNali.py

put the correct path such as

/nfs/users/nfs_z/zn1/src/merge/replace/replace-bin

in

path.append('/nfs/users/nfs_z/zn1/src/merge/replace/replace-bin') # find ssaha.py


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