phasebook is a novel approach for reconstructing the haplotypes of diploid genomes from long reads de novo, that is without the need for a reference genome.

References:

• Luo, Xiao, Xiongbin Kang, and Alexander Schönhuth. "phasebook: haplotype-aware de novo assembly of diploid genomes from long reads." Genome biology 22.1 (2021): 1-26.

• phasebook on GitHub

• Module Name: phasebook (see the modules page for more information)
• Use the $SLURM_CPUS_PER_TASK variable to set the appropriate number of threads. (See example below.)
• Environment variables set
  • $PHASEBOOK_TESTDATA points to a small test data set
• The online documentation suggest calling the main script like so: python phasebook.py. On our system it is incorrect to use the python prefix with this script due to the way it is installed.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c8 --mem=4g --gres=lscratch:10
salloc: Pending job allocation 33141417
salloc: job 33141417 queued and waiting for resources
salloc: job 33141417 has been allocated resources
salloc: Granted job allocation 33141417
salloc: Waiting for resource configuration
salloc: Nodes cn0881 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.33141417.0
slurmstepd: error: x11: unable to read DISPLAY value

[user@cn0881 ~]$ module load phasebook
[+] Loading phasebook  1.0.0  on cn0881
[+] Loading singularity  3.8.5-1  on cn0881

[user@cn0881 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0881 33141417]$ cp -r $PHASEBOOK_TESTDATA .

[user@cn0881 33141417]$ cd TESTDATA

[user@cn0881 TESTDATA]$ phasebook.py -i reads.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
use preset parameters...
2022-02-25 13:20:59,226 - /opt/phasebook/scripts/phasebook.py[line:262] - INFO: splitting input fastx file into 1 subfiles...
2022-02-25 13:20:59,361 - /opt/phasebook/scripts/phasebook.py[line:270] - INFO: splitting finished.
[...snip]
start polishing...
2022-02-25 13:22:26,529 - /opt/phasebook/scripts/phasebook.py[line:374] - INFO: All has been finished successfully.

2022-02-25 13:22:26,529 - /opt/phasebook/scripts/phasebook.py[line:375] - INFO: The final output haplotype aware contigs are here: ./contigs.fa

2022-02-25 13:22:26,529 - /opt/phasebook/scripts/phasebook.py[line:376] - INFO: Thank you for using phasebook!

[user@cn0881 TESTDATA]$ ls
1.split_fastx  3.cluster        5.polish          clustered_reads.list  phasebook.log  reference.fa
2.overlap      4.asm_supereads  all.supereads.fa  contigs.fa            reads.fa

[user@cn0881 TESTDATA]$ exit
exit
salloc: Relinquishing job allocation 33141417

[user@biowulf ~]$

Create a batch input file (e.g. phasebook.sh). For example:

#!/bin/bash
set -e
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}
cd /data/${USER}/phasebook/${SLURM_JOB_ID}
module load phasebook
phasebook.py -i /path/to/reads.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] phasebook.sh

Create a swarmfile (e.g. phasebook.swarm). For example:

mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; phasebook.py -i /path/to/reads1.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; phasebook.py -i /path/to/reads2.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; phasebook.py -i /path/to/reads3.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x
mkdir -p /data/${USER}/phasebook/${SLURM_JOB_ID}; cd !$; phasebook.py -i /path/to/reads4.fa -t $SLURM_CPUS_PER_TASK -p hifi -g small -x

Submit this job using the swarm command.

swarm -f phasebook.swarm [-g #] [-t #] --module phasebook