Table of Contents

FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds.

Information

Usage

See which versions of falcon-phase are available: 

$ module avail falcon-phase

Load one version into your environment: 

$ module load falcon-phase/git-7c50154e

Note: you need to copy and customize the example config.sh and config.json into your working directory. You will need to change the CPU parameters to match the number requested in your SLURM job as well as the paths to your data. I strongly recommend running this from the scratch directory on a compute node.

Consult the README for more information: https://github.com/phasegenomics/FALCON-Phase

Installation

Notes from the sysadmin during installation: 

$ cd /tmp
$ git clone --recursive https://github.com/phasegenomics/FALCON-Phase.git
$ cd FALCON-Phase/src
$ make
$ cd ..
$ sudo mkdir -p /export/apps/falcon-phase/git-7c50154e
$ sudo chown aorth:aorth /export/apps/falcon-phase/git-7c50154e
# modify configs for local environment
$ vim pipeline/config.sh
$ vim pipeline/config.json
$ cp -r bin LICENSE.txt pipeline README.md test_data tests validation /export/apps/falcon-phase/git-7c50154e
$ python3 -m venv /export/apps/falcon-phase/git-7c50154e/venv
$ source /export/apps/falcon-phase/git-7c50154e/venv/bin/activate
$ pip install numpy==1.14.2 biopython
$ sudo chmod +x /export/apps/falcon-phase/git-7c50154e/bin/preprocess_diploid_asm_for_fc_phase.py
$ sudo chown -R root:root /export/apps/falcon-phase/git-7c50154e

Test the installation with the included test data: 

$ interactive -c 8 -J falcon-PHASE
$ mkdir -p /var/scratch/aorth/2020-11-11-falcon-phase-test
$ cd /var/scratch/aorth/2020-11-11-falcon-phase-test
$ cp -r /export/apps/falcon-phase/git-7c50154e/pipeline/* .
# edit configs!!!
$ module load falcon-phase/git-7c50154e
$ preprocess_diploid_asm_for_fc_phase.py -P /export/apps/falcon-phase/git-7c50154e/test_data/cns_p_ctg.fasta -H /export/apps/falcon-phase/git-7c50154e/test_data/cns_h_ctg.fasta -o cleaned_contigs
$ snakemake -s snakefile --verbose -p