Longphase

Introduction

LongPhase is an ultra-fast program for simultaneously co-phasing SNPs and SVs by using Nanopore and PacBio long reads. It is capable of producing nearly chromosome-scale haplotype blocks by using Nanpore ultra-long reads without the need for additional trios, chromosome conformation, and strand-seq data. On an 8-core machine, LongPhase can finish phasing a human genome in 10-20 minutes.

For more information, please check:

Docker hub: https://hub.docker.com/r/alexanrna/longphase

Home page: https://github.com/twolinin/longphase

Versions

• 1.4

Commands

• longphase

Module

You can load the modules by:

module load biocontainers
module load longphase

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run longphase on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=longphase
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers longphase

longphase phase \
    -s SNP.vcf \
    --sv-file SV.vcf \
    -b alignment.bam \
    -r reference.fasta \
    -t 8 \
    -o phased_prefix \
    --ont # or --pb for PacBio Hifi