ILRI Research Computing

TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

• Version: 4.0
• Added: August, 2014
• Link: http://www.maizegenetics.net/tassel

See which versions of tassel are available:

$ module avail tassel

Load one version into your shell's environment:

$ module load tassel/4.0

• Tassel uses java with a default memory setting of: -Xms512m -Xmx1536m
• So you have to increase the maximum memory(-Xmx) to atleast 4GB otherwise tassel would run out of memory really fast
• Use the following options to set the maximum memory size to 4GB:

  -Xms512m -Xmx4096m

• For example:

  run_pipeline.pl -Xms512m -Xmx4096m

Notes from the sysadmin during installation:

$ git clone git://git.code.sf.net/p/tassel/tassel3-standalone tassel3
$ cd tassel3/
$ git checkout V3.0.165
$ sudo su -
$ mkdir -p /export/apps/tassel/3.0.165
$ cp -rv * /export/apps/tassel/3.0.165

Sample script for running via SLURM:

#!/bin/env bash

#SBATCH -p batch
#SBATCH -J tassel
#SBATCH -n 10

current_date=$(date +%b_%d)

DATADIR="/home/monyango/data/cullicoides_br/$current_date"

# create current_day folder
mkdir $DATADIR

#create UNEAK folder in $DATADIR
mkdir ${DATADIR}/UNEAK

#load tassel module
module load tassel/3.0.165

#sequence keys
illumina_sequence_data='/home/monyango/data/cullicoides_br/Co_s_5_sequence.txt.gz'
gbs_barcode_keys='/home/monyango/data/cullicoides_br/GBS_barcode_key.txt'

# step 1: create workingdirplugin - create several folders in DATADIR/UNEAK
run_pipeline.pl -Xmx4096m -fork1 -UCreatWorkingDirPlugin -w ${DATADIR}/UNEAK -endPlugin -runfork1

# copy sequence data to DATADIR/UNEAK/Illumina & key to DATADIR/UNEAK/key
cp ${illumina_sequence_data} ${DATADIR}/UNEAK/Illumina/
cp ${gbs_barcode_keys} ${DATADIR}/UNEAK/key/

# step 2: derive tagcount list
run_pipeline.pl -Xmx4096m -fork1 -UFastqToTagCountPlugin -w ${DATADIR}/UNEAK -e PstI -endplugin -runfork1

# step 3: merge tag count files of the same taxon
run_pipeline.pl -Xmx4096m -fork1 -UMergeTaxaTagCountPlugin -w ${DATADIR}/UNEAK -c 5 -endplugin -runfork1

# step 4: identify tag pairs for snip calling
run_pipeline.pl -Xmx4096m -fork1 -UTagCountToTagPairPlugin -w ${DATADIR}/UNEAK -e 0.03 -endplugin -runfork1

# step 5: generate tags by taxa file
run_pipeline.pl -Xmx4096m -fork1 -UTagPairToTBTPlugin -w ${DATADIR}/UNEAK -endplugin -runfork1

# step 6: generate map info file
run_pipeline.pl -Xmx4096m -fork1 -UTBTToMapInfoPlugin -w ${DATADIR}/UNEAK -endplugin -runfork1

# step 7: output hapmap file
run_pipeline.pl -Xmx4096m -fork1 -UMapInfoToHapMapPlugin -w ${DATADIR}/UNEAK -mnMAF 0.05 -mxMAF 0.5  -mnC 0 -mxC 1 -endplugin -runfork1