High-Performance Computing at the NIH
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ChangeoO on NIH HPC Systems

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin sequences, and reconstructing germline sequences.

Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of immunoglobulin (Ig) repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of T and B lymphocytes. Change-O is a suite of utilities to facilitate advanced analysis of Ig and TCR sequences following germline segment assignment. Change-O handles output from IMGT/HighV-QUEST and IgBLAST, and provides a wide variety of clustering methods for assigning clonal groups to Ig sequences. Record sorting, grouping, and various database manipulation operations are also included.

 

On Helix

Sample session:


[susanc@helix ~]$ module load changeo
[susanc@helix ~]$ DefineClones.py -h
usage: DefineClones.py [-h] [--version]  ...

Assign Ig sequences into clones

optional arguments:
  -h, --help  show this help message and exit
  --version   show program's version number and exit

subcommands:
              Cloning method
    bygroup   Defines clones as having same V assignment, J assignment, and
              junction length with specified substitution distance model.
    hclust    Defines clones by specified distance metric on CDR3s and cutting
              of hierarchical clustering tree

output files:
    clone-pass
        database with assigned clonal group numbers.
    clone-fail
        database with records failing clonal grouping.

required fields:
    SEQUENCE_ID, V_CALL or V_CALL_GENOTYPED, D_CALL, J_CALL, JUNCTION_LENGTH

    
        sequence field specified by the --sf parameter

output fields:
    CLONE

Batch job on Biowulf

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

#!/bin/bash
module load changeo

cd /data/$USER/dir
changeo commands

Then submit the file on biowulf

sbatch changeo.sh
Swarm of Jobs on Biowulf

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

# this file is called changeo.swarm
cd dir1;changeo commands
cd dir2;changeo commands
cd dir3;changeo commands
[...]

Submit this job using the swarm command.

swarm -f changeo.swarm --module changeo

Interactive job on Biowulf
Allocate an interactive session and run raremetal. Sample session:
[susanc@biowulf ~]$ sinteractive 
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[susanc@cn1719 ~]$ module load changeo

[susanc@cn1719 ~]$ changeo commends
Documentation
http://changeo.readthedocs.io/en/latest/