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

===== Information =====
  * Version: 5.2.77
  * Added: November, 2021
  * Link: https://www.maizegenetics.net/tassel

===== Usage =====
See which versions of tassel are available:

<code>$ module avail tassel</code>

Load one version into your shell's environment and run it:

<code>$ module load tassel/5.2.77
$ run_pipeline.pl</code>

**Note:** Tassel uses a default memory of ''-Xms512m -Xmx1536m'', so you will probably want to increase that so it doesn't crash, for example: ''run_pipeline.pl -Xms512m -Xmx4096m''

===== Sample Script =====
Sample sbatch script for running via SLURM, //tassel.sbatch//:

<file>#!/usr/bin/env bash

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

current_date=$(date +%Y-%m-%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</file>

==== Installation =====
Notes from the sysadmin during installation:

<code>$ git clone https://bitbucket.org/tasseladmin/tassel-5-standalone.git -b V5.2.77
$ cd tassel-5-standalone
$ sudo mkdir -p /export/apps/tassel/5.2.77
$ sudo cp -rv * /export/apps/tassel/5.2.77</code>