ABOUT THE DATASETS 

There are three Illumina simulated datasets: one standard dataset, two additional datasets, and a small test 
dataset. For each dataset, sequencing reads are in FASTQ files (*.fq) and the alignments of read and reference
are in ALN files (*.aln). For each paired‐read dataset, *1.fq contains data of the first reads, and *2.fq for
the second reads. Similarly, *1.aln has read alignments for the first reads and *2.aln for the second reads.
The FASTAQ and ALN formats are described in the Data File Format section below.  

READ ID CONVENTION 

A read id is in the form part1‐part2‐part3, where part1 is reference sequence id, part2 is a number assigned by
ART and unique to a paired‐end read pair, and part3 is either 1 for the first read or 2 for the second read.   

DATASETS

  For each paired-read dataset below, *1.fq.gz contains data of the first reads, and *2.fq.gz for the second reads.
  Similarly, *1.aln.gz has read alignments for the first reads and *2.aln.gz for the second reads.   

  STANDARD DATASETS
	Read type: 35bp x 2 (paired-end reads)
	Read fragment size distribution: Gaussian (MEAN 200, STD 20) 
 
	1) 6 trio individuals, 60X each 
		chr17p12_trio_60x1.fq.gz
		chr17p12_trio_60x1.aln.gz
		chr17p12_trio_60x2.fq.gz
		chr17p12_trio_60x2.aln.gz
	2) 1,000 unrelated individuals, 4X each 
		chr17p12_1000_4x1.fq.gz
		chr17p12_1000_4x1.aln.gz
		chr17p12_1000_4x2.fq.gz
		chr17p12_1000_4x2.aln.gz

  ADDITIONAL DATASET #1

	Read type: 35bp x 2 (paired-end reads)
	Read fragment size distribution: Gaussian (MEAN 200, STD 20) 

	1) 200 individuals, 4X each 
		Subjects: first 66 from pop0, first 67 from pop1, first 67 from pop3 in the 1,000 unrelated individuals above 
		chr17p12_200_4x1.fq.gz
		chr17p12_200_4x1.aln.gz
		chr17p12_200_4x2.fq.gz 
		chr17p12_200_4x2.aln.gz

	2) 100 individuals, 8X each
		Subjects: first 33 from pop0, first 33 from pop1, first 34 from pop3 in the 1,000 unrelated individuals above
		chr17p12_100_8x1.fq.gz
		chr17p12_100_8x1.aln.gz
		chr17p12_100_8x2.fq.gz 
		chr17p12_100_8x2.aln.gz

  ADDITIONAL DATASET #2: 
	Subject: a single trio individual
	Read type: 35bp x 2 (paired-end reads)

	1) a single trio individual, 60X, fragment size: mean 500, STD 50
		aTrio_child_5h60x1.fq.gz 
		aTrio_child_5h60x1.aln.gz
		aTrio_child_5h60x2.fq.gz 
		aTrio_child_5h60x2.aln.gz

	2) the same trio individual, 60X, fragment size: mean 3000, STD 300 
		aTrio_child_3k60x1.fq.gz
		aTrio_child_3k60x1.aln.gz
		aTrio_child_3k60x2.fq.gz
		aTrio_child_3k60x2.aln.gz

  A SMALL TEST DATASET (for data validation only) 
	Read type: 35bp x 2 (paired-end reads)
	Read fragment size distribution: Gaussian (MEAN 200, STD 20) 
 
	1) 6 trio individuals, 8X each 
		test_trio_200_20_8x1.fq.gz
		test_trio_200_20_8x1.aln.gz
		test_trio_200_20_8x2.fq.gz
		test_trio_200_20_8x2.aln.gz

SIMULATION TOOL 

	ART (Artificial Read Transcriber), version 0.8.1.6 

READ ERROR PROFILE 

	The read error profile is based on the empirical error model derived from the calibrated Illumina paired-end read data by Richard Durbin group at Sanger.

FRAGMENT SIZE DISTRIBUTION 

	The fragment sizes of all paired‐end reads data above follow the Gaussian distribution.  

DATA FILE FORMAT

	FASTQ format 
		A FASTQ file contains both sequence bases and quality scores of sequencing reads and is in the following format:  
			@read_id 
			sequence_read 
			+ 
			base_quality_scores 
	
		A base quality score is coded by the ASCII code of a single character, where the quality score is equal to ASCII code of the
       		character minus 33.    

		Example: 
		@pop0_ind0_chr0-4028550-1 
		caacgccactcagcaatgatcggtttattcacgat 
		+ 
		????????????7?????<??>??=&?<<?-<?0?

	ALN format 
		>ref_seq_id	read_id	aln_start_pos	ref_seq_strand
	       	ref_seq_aligned
	       	read_seq_aligned 
	
		aln_start_pos is the alignment start position of reference sequence. aln_start_pos is always relative to the strand of reference
       		sequence. That is, aln_start_pos 10 in the plus (+) strand is different from aln_start_pos 10 in the minus (‐) stand.  
	
		ref_seq_aligned is the aligned region of reference sequence, which can be from plus strand or minus strand of the reference sequence.  
		read_seq_aligned is the aligned sequence read, which always in the same orientation of the same read in the corresponding fastq file. 

		Example: 
		>pop0_ind348_chr0	pop0_ind348_chr0-4028548-1	2644400	+ 
		gtaccatacttccttagtcgtgtactcttggtcta 
		gtaccatacttccttagtcgtgtacgcttggtcta 
		>pop0_ind348_chr0	pop0_ind348_chr0-4028550-1	4557676	- 
		ttcatgggggctccttcacgtatgactgaaaagtg 
		ttcatgggggctccttcacgtatgactgaaaagtg