A basic tool to split the specified barcoded reads out from a set of FASTQ files. Maul also corrects the read names to reflect the first and second read of a pair, required for Picard and other downstream tools. Maul can handle single and dual barcoded runs. The input is expected to be in either fastq or gziped fastq files (ending in .fq.gz). The input files need to be separated into three or four files:

• one fastq for the first sequenced read
• one fastq for the second read (optional)
• one or two fastqs respectively for single or dual barcoded libraries.

Maul optionally outputs a file with read counts for each barcode combination, as well as a sorted histogram file for unknown barcodes that were seen during parsing. The maximum edit distance can be set for barcodes allowing X number of mismatches. Be careful with this parameter, as many barcode libraries are designed with an edit distance of 3 between individual barcodes, so setting this parameter above 1 could result in barcode switches. Set this to zero if you'd like to be more stringent about barcode parsing.

Building

You need to have Java 1.7 and SBT installed. Once you do, just type:

sbt compile

to build the tool, and

sbt assembly

to make a single jar version with all of the dependencies built in

Running a single-barcoded file

An important note: this implicitly sets the edit distance to 1 (default), if you want to more or less stringent barcode splitting, you should set the maxDistance parameter. Again, it's dangerous to go much above 1 without specificly designed barcodes.

java -jar <path_to_maul_jar>.jar \
--inFQ1 <reads1>.fq.gz \
--inFQ2 <reads2>.fq.gz \
--inBarcodeFQ1 <barcodereads1>.fq.gz \
--outFQ1 <outputreads1>.fq.gz \
--outFQ2 <outputreads2>.fq.gz \
--barcodes1 CGATGT,TGACCA,CTTGTA,GTGAAA \
--barcodeStatsFile statsFile.txt \
--barcodeStatsFileUnknown statsUnkownFile.txt

Running a dual-barcoded file

(barcode matching distance again allowed to be one)

java -jar <path_to_maul_jar>.jar \
--inFQ1 <reads1>.fq.gz \
--inFQ2 <reads2>.fq.gz \
--inBarcodeFQ1 <barcodereads1>.fq.gz \
--inBarcodeFQ2 <barcodereads2>.fq.gz \
--outFQ1 <outputreads1>.fq.gz \
--outFQ2 <outputreads2>.fq.gz \
--barcodes1 CGATGT,TGACCA,CTTGTA,GTGAAA \
--barcodes2 TGATGT,TTACCA,TTTGTA,TTGAAA \
--barcodeStatsFile statsFile.txt \
--barcodeStatsFileUnknown statsUnkownFile.txt