The PBSuite contains two projects created for analysis of Pacific Biosciences long-read sequencing data: PBHoney and PBJelly.

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

References:

• English AC, Richards S, Han Y, Wang M, Vee V, et al. (2012) Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLOS ONE 7(11): e47768. doi:10.1371/journal.pone.0047768
• English A.C., Salerno W.J. & Reid J.G. (2014) PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics 15, 180. doi:10.1186/1471-2105-15-180

• PBSuite Homepage
• $PBSUITE_HOME/docs

• Module Name: pbsuite or pbjelly (see the modules page for more information)
• Environment variables set
  • PBSUITE_HOME
• Example files in $PBSUITE_HOME/docs/honeyExample/ and $PBSUITE_HOME/docs/jellyExample/

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

PBHoney

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pbsuite
[user@cn3144 ~]$ cp $PBSUITE_HOME/docs/honeyExample/* .
[user@cn3144 ~]$ sh workflow.sh
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

PBJelly

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pbsuite
[user@cn3144 ~]$ cp -r $PBSUITE_HOME/docs/jellyExample/* .
[user@cn3144 ~]$ sed -i "s|/__PATH__/_TO_/jellyExample|$PWD|g" Protocol.xml
[user@cn3144 ~]$ for stage in setup mapping support extraction assembly output
do
    Jelly.py $stage Protocol.xml
done

[user@cn3144 ~]$ summarizeAssembly.py jelly.out.fasta # check your results
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/sh
set -e
module load pbsuite

for stage in setup mapping support extraction assembly output
do
    Jelly.py $stage Protocol.xml
done

Submit this job using the Slurm sbatch command.

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

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

for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol1.xml || exit 1; done
for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol2.xml || exit 1; done
for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol3.xml || exit 1; done
for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol4.xml || exit 1; done

Submit this job using the swarm command.

swarm -f pbjelly.swarm [-g #] [-t #] --module pbsuite