Wakhan is a tool for analyzing chromosome-level changes in DNA using long reads from Oxford Nanopore or PacBio. It uses aligned long reads and phased variants to identify differences between haplotypes. The hapcorrect module corrects errors by using copy number differences. Wakhan also estimates the purity and ploidy of the sample and creates interactive plots showing haplotype-specific copy numbers and coverage.

References:

• Tanveer Ahmad, Mikhail Kolmogorov, Ayse Keskus, Ataberk Ataberk Donmez, Midhat Farooqi. Haplotype-specific copy number profiling from long reads sequencing data. Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts).

• wakhan Main Site

This application requires a graphical connection using NX

• Module Name: wakhan (see the modules page for more information)
• Environment variables set
  • WAKHAN_HOME
  • WAKHAN_EXAMPLES
• Example files in $WAKHAN_EXAMPLES

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

[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 wakhan

[user@cn3144 ~]$  

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load wakhan
wakhan < wakhan.in > wakhan.out

Submit this job using the Slurm sbatch command.

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

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

wakhan < wakhan.in > wakhan.out
wakhan < wakhan.in > wakhan.out
wakhan < wakhan.in > wakhan.out
wakhan < wakhan.in > wakhan.out

Submit this job using the swarm command.

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