diff --git a/renameFastQs.bash b/renameFastQs.bash
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+++ b/renameFastQs.bash
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+#!/bin/bash
+
+#
+##
+### Environment and bash sanity.
+##
+#
+set -u
+set -e
+umask 0027
+SCRIPT_NAME=$(basename $0)
+if [[ "${BASH_VERSINFO}" -lt 4 || "${BASH_VERSINFO[0]}" -lt 4 ]]
+then
+	echo "Sorry, you need at least bash 4.x to use ${SCRIPT_NAME}." >&2
+	exit 1
+fi
+
+#
+# Make sure dots are used as decimal separator.
+#
+LANG='en_US.UTF-8'
+LC_NUMERIC="${LANG}"
+
+#
+# Trap all exit signals: HUP(1), INT(2), QUIT(3), TERM(15), ERR
+#
+trap '_reportError $LINENO' HUP INT QUIT TERM EXIT ERR
+
+#
+##
+### Functions.
+##
+#
+
+function _Usage() {
+	echo
+	echo 'Script to rename all FastQs matching a specified pattern in the current directory'
+	echo 'from GenomeScan FastQ naming conventions to UMCG Genetics dept. FastQ naming conventions.'
+	echo
+	echo "    ${SCRIPT_NAME} [options]"
+	echo
+	echo " Options:"
+	echo "    -v                         Enable verbose logging (optional)."
+	echo "    -s YYMMDD                  sequencingStartDate"
+	echo "    -f 'FastQ_filename_regex'  Regex pattern to find the FastQ files that must be renamed."
+	echo "                               Note: the pattern must be single quoted to prevent expansion by the shell."
+	echo "                               E.g. -f 'HTVTYBBXX_103373-003*'"
+	echo
+}
+
+function _reportError() {
+	local _problematicLine="${1}"
+	local _exitStatus="${2:-$?}"
+	local _errorMessage="Unknown error."
+	_errorMessage="${3:-${_errorMessage}}"
+	#
+	# Notify on STDOUT.
+	#
+	echo "
+$(hostname) - ${SCRIPT_NAME}:${_problematicLine}: FATAL: exit code = ${_exitStatus}
+$(hostname) - ${SCRIPT_NAME}:${_problematicLine}:        error message = ${_errorMessage}
+"
+	#
+	# Reset trap and exit.
+	#
+	trap - EXIT
+	exit ${_exitStatus}
+}
+
+function _RenameFastQ() {
+	local _fastqPath="${1}"
+	local _sequencingStartDate="${2}"
+	echo "INFO: Processing FastQ ${_fastqPath}..."
+	#
+	# Example for FastQs from external lab:
+	#  1. GenomeScan FastQ file name format:
+	#         Flowcell_Customer-BatchNumber-SampleNumber_Barcode1-Barcode2_Lane_Read.fastq.gz
+	#     E.g.:
+	#         HTVTYBBXX_103373-003-001_AGGCAGAA-AGGCTTAG_L001_R1.fastq.gz
+	#
+	# Example of sequence read header line as found in Illumina FastQ files produced with Casava / bcl2fastq >= 1.8:
+	#         @sequencer:run:flowcell:lane:tile:xCoordinateOfClusterInTile:yCoordinateOfClusterInTile sequenceReadOfPair:filtered:barcode[+barcode2]
+	#     E.g.:
+	#         @K00296:315:HVLN7BBXX:7:1101:2940:1173 1:Y:0:GTAGAGGA+TCTACTAT
+	#
+	#
+	local _fastqDir="$(dirname "${_fastqPath}")"
+	local _fastqFile="$(basename "${_fastqPath}")"
+	
+	#
+	# Do NOT parse filenames: get the essential stuff from the sequence read IDs instead
+	#
+	#local _regex='^([A-Z0-9]*XX)_(103373-[0-9][0-9]*-[0-9][0-9]*)_([ATCG][ATCG]*-[ATCG][ATCG]*)_L00([1-8])_R([12]).fastq.gz$'
+	#if [[ "${_fastqFile}" =~ ${_regex} ]]
+	#then
+	#	local _flowcell="${BASH_REMATCH[1]}"
+	#	local _customerBatchSampleCombi="${BASH_REMATCH[2]}"
+	#	local _barcodes="${BASH_REMATCH[3]}"
+	#	local _lane="${BASH_REMATCH[4]}"
+	#	local _sequenceReadOfPair="${BASH_REMATCH[5]}"
+	#	if [[ "${enableVerboseLogging}" -eq 1 ]]
+	#	then
+	#		echo "DEBUG:    Found _flowcell ............... = ${_flowcell}"
+	#		echo "DEBUG:    Found _customerBatchSampleCombi = ${_customerBatchSampleCombi}"
+	#		echo "DEBUG:    Found _barcodes ............... = ${_barcodes}"
+	#		echo "DEBUG:    Found _lane ................... = ${_lane}"
+	#		echo "DEBUG:    Found _sequenceReadOfPair ..... = ${_sequenceReadOfPair}"
+	#	fi
+	#else
+	#	echo "FATAL: Failed to parse filename for ${_fastq}"
+	#	exit 1
+	#fi
+	
+	local _firstReadID=$(zcat "${_fastqPath}" | head -1)
+	if [[ "${enableVerboseLogging}" -eq 1 ]]
+	then
+		echo "DEBUG:    Found _firstReadID ............ = ${_firstReadID}"
+	fi
+	local _regex='^@([A-Z0-9][A-Z0-9]*):([0-9][0-9]*):([A-Z0-9][A-Z0-9]*XX):([1-8]):[0-9]*:[0-9]*:[0-9]* ([1-2]):[YN]:[0-9][0-9]*:[ATCGN][ATCGN+]*'
+	if [[ "${_firstReadID}" =~ ${_regex} ]]
+	then
+		local _sequencer="${BASH_REMATCH[1]}"
+		local _run="${BASH_REMATCH[2]}"
+		local _flowcell="${BASH_REMATCH[3]}"
+		local _lane="${BASH_REMATCH[4]}"
+		local _sequenceReadOfPair="${BASH_REMATCH[5]}"
+		#
+		# Note: we do require the ID of the first read to contain a DNA barcode at the end,
+		# but we don't parse barcodes here. Due to sequencing errors the barcode may deviate slightly.
+		# Instead we parse the barcodes from the first reads and determine the most abundant one later on.
+		#
+		
+		#
+		# Sanity check for run number and add leading zero when 3 < run number < 4.
+		#
+		if [[ "${#_run}" -lt 3 ]]
+		then
+			echo "FATAL: run number detected in ID of first read is too short (< 3): ${_run}"
+			exit 1
+		elif [[ "${#_run}" -eq 3 ]]
+		then
+			_run="0${_run}"
+		fi
+		if [[ "${enableVerboseLogging}" -eq 1 ]]
+		then
+			echo "DEBUG:    Found _sequencer .............. = ${_sequencer}"
+			echo "DEBUG:    Found _run .................... = ${_run}"
+			echo "DEBUG:    Found _flowcell ............... = ${_flowcell}"
+			echo "DEBUG:    Found _lane ................... = ${_lane}"
+			echo "DEBUG:    Found _sequenceReadOfPair ..... = ${_sequenceReadOfPair}"
+		fi
+	else
+		echo "FATAL: Failed to required meta-data values from ID of first read of ${_fastqPath}"
+		exit 1
+	fi
+	
+	local _mostAbundandBarcode=$(zcat "${_fastqPath}" | head -4000 | awk 'NR % 4 == 1' | awk -F ':' '{print $10}' | sort | uniq -c | sort -k 1,1nr | head -1 | awk '{print $2}' | tr -d '\n')
+	local _barcodeRegex='^([ATCG][ATCG+]*)$'
+	if [[ "${_mostAbundandBarcode}" =~ ${_barcodeRegex} ]]
+	then
+		local _barcodes="${BASH_REMATCH[1]}"
+		#
+		# In case the sample was double barcoded change the separator from '+' to '-'.
+		#
+		_barcodes="${_barcodes/+/-}"
+		if [[ "${enableVerboseLogging}" -eq 1 ]]
+		then
+			echo "DEBUG:    Found _barcode(s) ............. = ${_barcodes}"
+		fi
+	elif [[ "${_mostAbundandBarcode}" =~ N ]]
+	then
+		echo "ERROR: Most abundant barcode(s) in max first 1000 reads contains Ns: ${_barcodes}"
+		echo "ERROR: Skipping discarded FastQ ${_fastqFile} due to poor sequencing quality of barcode(s)."
+		return
+	else
+		echo "ERROR: Failed to determine the most abundant barcode(s) from the max first 1000 reads."
+		echo "FATAL: Failed to process FastQ ${_fastqFile} due to poor sequencing quality of barcode(s)."
+		exit 1
+	fi
+	
+	local _fastqChecksum=$(cat "${_fastqDir}/"*.md5 | grep "${_fastqFile}" | awk '{print $1}')
+	local _newFastqDir="${_fastqDir}/${_sequencingStartDate}_${_sequencer}_${_run}_${_flowcell}"
+	local _newFastqFile="${_sequencingStartDate}_${_sequencer}_${_run}_${_flowcell}_L${_lane}_${_barcodes}_${_sequenceReadOfPair}.fq.gz"
+	
+	#
+	# Create sequence run subdir if it did not already exist.
+	#
+	mkdir -p "${_newFastqDir}"
+	
+	#
+	# Check if new FastQ file path does not already exist to prevent overwriting a sample with another one.
+	#
+	if [[ -e "${_newFastqDir}/${_newFastqFile}" ]]
+	then
+		echo "FATAL: ${_newFastqDir}/${_newFastqFile} already exists."
+		echo "FATAL: will NOT move ${_fastqPath} -> ${_newFastqDir}/${_newFastqFile}."
+		exit 1
+	fi
+	
+	#
+	# Move and rename FastQ + MD5 checksum on the fly.
+	#
+	echo "INFO:    Moving ${_fastqPath} -> ${_newFastqDir}/${_newFastqFile}"
+	printf '%s  %s\n' "${_fastqChecksum}" "${_newFastqFile}" > "${_newFastqDir}/${_newFastqFile}.md5"
+	mv "${_fastqPath}" "${_newFastqDir}/${_newFastqFile}"
+}
+
+#
+##
+### Main
+##
+#
+
+#
+# Get commandline arguments.
+#
+enableVerboseLogging=0 # Disabled by default.
+while getopts "s:f:hv" opt
+do
+	case $opt in
+		h)
+			_Usage
+			#
+			# Reset trap and exit.
+			#
+			trap - EXIT
+			exit 0
+			;;
+		s)
+			sequencingStartDate="${OPTARG}"
+			;;
+		f)
+			fastqFilePattern="${OPTARG}"
+			;;
+		v)
+			enableVerboseLogging=1
+			;;
+		\?)
+			_reportError ${LINENO} '1' "Invalid option -${OPTARG}. Try \"$(basename $0) -h\" for help."
+			;;
+		:)
+			_reportError ${LINENO} '1' "Option -${OPTARG} requires an argument. Try \"$(basename $0) -h\" for help."
+			;;
+	esac
+done
+
+#
+# Make sure there are no extra arguments we did not expect nor need.
+#
+shift $(($OPTIND - 1))
+if [[ ! -z ${1:-} ]]
+then
+	_reportError ${LINENO} '1' "Invalid argument \"$1\". Try \"$(basename $0) -h\" for help."
+fi
+
+#
+# Check if required args are present.
+#
+if [[ -z "${sequencingStartDate:-}" || -z "${fastqFilePattern:-}" ]]
+then
+	 _reportError ${LINENO} 1 "One ore more required arguments is missing. Try \"$(basename $0) -h\" for help."
+fi
+
+#
+# Check if sequencingStartDate is in the expected format.
+#
+ssd_regex='^[1-9][0-9][0-1][1-9][0-3][0-9]$'
+if [[ "${sequencingStartDate}" =~ ${ssd_regex} ]]
+then
+	echo "INFO: Using sequencingStartDate ${sequencingStartDate}"
+else
+    _reportError ${LINENO} 1 "sequencingStartDate in unsupported format. Must be YYMMDD, but got ${sequencingStartDate}."
+fi
+
+#
+# Process FastQ files.
+#
+for FastQ in $(ls -1 ${fastqFilePattern})
+do
+	_RenameFastQ "${FastQ}" "${sequencingStartDate}"
+done
+
+#
+# Reset trap and exit.
+#
+echo "INFO: Finished successfully!"
+trap - EXIT
+exit 0
\ No newline at end of file