Software: LongPhase
Description
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs and SVs by using Nanopore and PacBio long reads.
Available Versions
| Unspecified: | 1.4 |
|---|
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.
Docker hub: https://hub.docker.com/r/alexanrna/longphase
Home page: https://github.com/twolinin/longphase
Commands
- longphase
Module
You can load the modules by:
module load biocontainers
module load longphase
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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