Pipeline Idea Download NCBI nr database Build Diamond database from nr Run Diamond Blastx on each pair of sample fastq files, generating 2 daa file Run daa2rma from each pair to generate single rma file per sample Use Meganizer About paired Read "The only way to do a paired-end analysis is to use the daa2rma tool which will create a new single .rma file from your two input .daa files. This program has command-line options to setup paired-read import. Use the options:

Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. Generic Trimmomatic command: java -jar trimmomatic-0.39.jar PE inputforward.fq.gz inputreverse.fq.gz outputforwardpaired.fq.gz outputforwardunpaired.fq.gz outputreversepaired.fq.gz outputreverseunpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36 Created a bash script for running trimmomatic on multiple files at the same time: This scripts looks for files with "_R1.fastq.gz" in their name, and applies trimmomaic on them, and their paired "_R2.fastq.gz" files in the same directory

Creating the sample FASTQ Files Set 1 These samples are Zymo MMC gDNA samples, sequenced as part of pilot run for GI project at JPL. mv SH5203_FT-SA29139_S11_L002_R1_001.fastq.gz sample1_R1.fastq.gz mv SH5203_FT-SA29139_S11_L002_R2_001.fastq.gz sample1_R2.fastq.gz mv SH5203_FT-SA29140_S12_L002_R1_001.fastq.gz sample2_R1.fastq.gz mv SH5203_FT-SA29140_S12_L002_R2_001.fastq.gz sample2_R2.fastq.gz