The FASTq Processor takes the Raw FASTQ files generated from Illumina NGS platforms and creates a directory containing fastq files for each individual sample. The input files required by the user are the unzipped Read 1 and Read 2 fastq files as well as the corresponding mapping file. The output directory will contain a new Read 1 and Read 2 fastq file for each sampleID as well an additional directory containing the index file.
This tool was created in order to assist users who are interested in using mothur in order to process their 16s rRNA gene sequences. The output directory can be referenced by the mothur make.file command, which will generate the necessary files to proceed with the mothur MiSeq workflow. The necessary index and oligos file are also provided should you choose to not to use the mothur make.file command.
For those users interested in using Qiime to process their Illumina amplicon sequences, we have generated a set of shell scripts to assist in the process of taking the raw fastq files and generating the seqs.fna file necessary to proceed with bacterial diversity analysis.