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make.contigs的功能在于将PE reads组装成tag
1、-file,可支持2、3、4列包含fq的格式
1)2列的格式如下:
reads1和reads2,与oligos文件配合用于数据分析( This type can be used with an oligos file create a group file for your dataset. )
small.forward.fastq small.reverse.fastq
test.forward2.fastq test.reverse2.fastq...
2)3的格式如下:将barcode、primer等在测序数据中进行了去除,并进行了拆分。
第一列表示样品(group),第二列表示reads1,第三列表示reads2
F8D0 F8D0_S345_L001_R1_001.fastq F8D0_S345_L001_R2_001.fastq
F8D125 F8D125_S358_L001_R1_001.fastq F8D125_S358_L001_R2_001.fastq
F8D141 F8D141_S359_L001_R1_001.fastq F8D141_S359_L001_R2_001.fastq
F8D142 F8D142_S360_L001_R1_001.fastq F8D142_S360_L001_R2_001.fastq
F8D143 F8D143_S361_L001_R1_001.fastq F8D143_S361_L001_R2_001.fastq
F8D144 F8D144_S362_L001_R1_001.fastq F8D144_S362_L001_R2_001.fastq
F8D145 F8D145_S363_L001_R1_001.fastq F8D145_S363_L001_R2_001.fastq
F8D146 F8D146_S364_L001_R1_001.fastq F8D146_S364_L001_R2_001.fastq
F8D147 F8D147_S365_L001_R1_001.fastq F8D147_S365_L001_R2_001.fastq
F8D148 F8D148_S366_L001_R1_001.fastq F8D148_S366_L001_R2_001.fastq
F8D149 F8D149_S367_L001_R1_001.fastq F8D149_S367_L001_R2_001.fastq
F8D150 F8D150_S368_L001_R1_001.fastq F8D150_S368_L001_R2_001.fastq...
My.forward.fastq My.reverse.fastq none My.index.fastq
2、- ffastq && rfastq
@M00704:50:000000000-A3G0K:1:1101:15777:1541 1:N:0:0NAGAGAGGATCT+#>>3A3A>CFFF
@M00704:50:000000000-A3G0K:1:1101:15370:1541 1:N:0:0NAGAGAGGATCT+#>>ABCCCFFFF...
7、-oligos
此文件中主要包含primer和barcode的信息,每行的开头必须是primer、barcode,或者是
#primer CCTACGGGAGGCAGCAG ATTACCGCGGCTGCTGG
V3primer ATTAGAWACCCBDGTAGTCCCCCGTCAATTCMTTTRAGT
V5primer ACTYAAAKGAATTGACGGGACRACACGAGCTGACGAC
V6BARCOD Eccaaccactg
F01R2ABARCODE ccaacaacca
F01R2BBARCODE ccaactgtca
F01R2CBARCODE ccaacaaacc
F01R2D...
应用例子
9、-bdiffs && pdiffs && tdiffs
10、-match && mismatch && gapopen && gapextend
11、-insert
12、-deltaq
13、-processors
14、-allfiles
15、trimoverlap
16、 *.contigs.report的格式解读
17、使用实例
mothur > make.contigs(ffastq=test_1.fastq, rfastq=test_2.fastq)
mothur > make.contigs(file=combo.fastq)
mothur > make.contigs(ffasta=test_1.fasta, rfasta=test_2.fasta)
mothur > make.contigs(ffasta=test_1.fasta, rfasta=test_2.fasta, rqfile=test_1.qual, fqfile=test_1.qual)
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