CAUS

Pipeline for Chromosome Assignment Using Synteny and it also fixes 3D-DNA's contig problems

Say if you have two assemblies target.fasta and reference.fasta

You want to assign scaffolds in target.fasta to the reference assembly reference.fasta:

How to run

    /tmp/casu/src/caus target.fasta reference.fasta assign.fasta > try.out

This gives you the assigned assembly file: assign.fasta

Note:

1. you need to give the full path of the caus  file.                     \
2. target.fasta and reference.fasta should be in your working directory. \
3. If you have a Segmentation fault (core dumped), please use try this   \

     /tmp/casu/caus -len 1000000 arget.fasta reference.fasta assign.fasta > try.out

Download and Compile:

Requirements for compiling: gcc

$ git clone https://github.com/wtsi-hpag/caus.git
$ cd caus
$ bash install.sh 

Running with 3D-DNA

3D-DNA is a popular HiC scaffolding pipeline. However, it makes so many breakpoints when examining HiC coverage profile. After scaffolding with 3D-DNA, contigs are sometimes fragmented. You can run caus to fix this problem.

Say you have contigs.fasta scaffolds-3D-DNA.fasta

/tmp/casu/src/caus contigs.fasta scaffolds-3D-DNA.fasta scaffolds-caus3D.fasta > try.out

Here

contigs.fasta is produced with long or short reads;       \ 
scaffolds-3D-DNA.fasta is an output file from 3D-DNA;     \
scaffolds-caus3D.fasta is a new scaffolding file.         \

More detailed information and examples can be found in the PPT file.

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