The command reads a fastq file and creates a fasta and quality file or can be used to parse fastq files by sample.

Default settings

The command parameters are file, fastq, fasta, qfile, oligos, group and format; file or fastq is required.

mothur >


mothur >



The file lines can be 2, 3, or 4 columns. The forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file, or forward fastq file then reverse fastq then forward index and reverse index file. If you only have one index file add ‘none’ for the other one.

Two Column 
ffastqfile1 rfastqfile1
ffastqfile2 rfastqfile2

Two Column PacBio

group1 pacBioFastqfile1 
group2 pacBioFastqfile2 
group3 pacBioFastqfile3
Three Column
group ffastqfile  rfastqfile
group ffastqfile  rfastqfile
group ffastqfile  rfastqfile
Four Column  - ('none' is the option for no forward index file)
My.forward.fastq My.reverse.fastq none My.rindex.fastq


The oligos parameter allows you to provide an oligos file to split your fastq file into separate fastq files by barcode and primers.

bdiffs & pdiffs & ldiffs & sdiffs & tdiffs

These parameters are used to allow differences in the barcode, primers, linkers and spacers. pdiffs is maximum number of differences to the primer sequence, default=0. bdiffs is maximum number of differences to the barcode sequence, default=0. ldiffs is maximum number of differences to the linker sequence, default=0. sdiffs is maximum number of differences to the spacer sequence, default=0. tdiffs is maximum total number of differences to the barcode, primer, linker and spacer (default to pdiffs + bdiffs + ldiffs + sdiffs).


If you are running the command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can’t find the barcodes and primers, it will search the reverse compliment.


The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.


The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.


When pacbio is set to true, quality scores of 0 will results in a corresponding base of N. Default=F.


The format parameter is used to indicate whether your sequences are sanger, solexa, illumina or illumina1.8+. default=sanger.