GenomeSequenceSimulator

GSS is a small tool for simulating sequence reads from a reference genome. A

INSTALL

Simple build by cmake .

Here is a build example. Enter src directory:

    mkdir build
    cd build
    cmake ..
    make

Binary execute file in bin/Bin/GSS

EXAMPLE

After build success ,enter example directory and run example.sh script.

QUICK START

Run GSS with config.json file . All infomations are within config.json.

Here is the config.json from example

{                                       #Top level is a object !
    "filePath": "./sequence.fasta",     #Basic genome file. 
    "fileType": "fasta",                #Genome file type.Only support fasta now.
    "variable":0.0001,                   
    "InDel":0.015,   
    "InDel_Extern":0.3,
    "error":0.0001,
    "output": [                         #Array of all simulator infos.
        {
            "file_name":"f0",           #Output name prefix.
            "file_type":"fastq",        #Output file type,support fasta and fastq
            "read_type": "single",      #
            "read_len": 100,            #
            "insert_len": 100,          #
            "depth":80                  #The expect depth of Nucleotide.
        },
        {
            "file_name":"f1",
            "file_type":"fastq",
            "read_type": "pair-end",
            "read_len": 100,
            "depth":100,
            "insert_len": 250
        }
    ]
}

OUTPUT

Here is the top 10 lines of each file that generated by above config.json

==> f0.fastq <==
@NC_007205.1_503982_504082_0:0:0_0/2
CTGGAACGGAGTATTCGTTTTAAAAGAGGGTGTATAAGTTTTAAAAAAAAATATTTAAGAACTATAAATATTTAACAAAAAAAATAAAGAAATATAAAAA
+
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
@NC_007205.1_430241_430341_0:0:0_1/2
TTTTATCAATTTTTTTTATTTAAATAGAATCAACCAAGTTCATACCCTCGCACCGAGAGGAATTTAGTTAAATTTATAAAATTTCTAGTTTAATTTCCAA
+
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
@NC_007205.1_1139113_1139213_0:0:0_2/1
ATACATAATAAGCACTATCTCTAAAGGATTTTTTTATTTGTTTTTTAGCATTATAAATTTCAATAAATGCATTTCTCATACTATCTTCTAGACCTGAAAA

==> f1_0.fastq <==
@NC_007205.1_1137336_1137436_0:0:0_0/1
CTTACACAATTATTTTGGTAGGCAATTTTACCTCTAGCAATCATTAATTGAGAATCTCTTGTGATTGGATAATGATTATCAGAATAAGAAATGCTACTTA
+
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
@NC_007205.1_706428_706528_0:0:0_1/2
AAAATTCAGAGGAACTCCGTAACTTTTACCTAACACTGATTTAAGTTAAAATAATCAATGAAGTAAAAAAAGTTTGTAACCTATTAGTTGTTGGGTTGTT
+
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
@NC_007205.1_555447_555547_0:0:0_2/2
TTTATGCCTACCTACGGTGGAGTAGGATGATGTATAAAGAATTCTTTTAAATAAATATTTCAACCTTTCAAATTATGTTTAATATTTTATAGGAGACTGA

==> f1_1.fastq <==
@NC_007205.1_1138736_1138836_0:0:0_0/2
ATTCATCTCGGATATATGGTTTGAGATTAGATAGAAAATAATCAAAATAATTTCAATGGAAACTATTTCCCCATTACTACTTACGTTGTAATCGATTACC
+
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
@NC_007205.1_705028_705128_0:0:0_1/1
TATGGCAAAATATTTGAATTCATATATAAAATTGACAAGATTAGTTTAAAAAAAAAGAAATCTATCGATTTTAAAATTATTAATGAAGCTCTTGAGGAAT
+
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
@NC_007205.1_554047_554147_0:0:0_2/1
TTTGATAGATTTTTAAGTTTTAAAAAATCTTTAGACCTAATTTCAAAAACTGGAATATTTATTTTTGATAATTCTGAAGGATATAATGAACCAAGAGATA