### OBITools Pipeline for raw sequence data analysis for sequencing data KD079 (see documentation in Boyer et al. 2016) illuminapairedend 150430_SND104_A_L008_HUA-3_R1.fastq -r 150430_SND104_A_L008_HUA-3_R2.fastq > pairedend_KD079.fastq obigrep -p 'mode!="joined"' pairedend_KD079.fastq > pairedend_KD079_joined.fastq obigrep -p 'ali_length>10' pairedend_KD079_joined.fastq > pairedend_KD079_joined_10.fastq ngsfilter -t tagfile_KD079.txt -u unidentified_KD079.fastq pairedend_KD079_joined_10.fastq > pairedend_KD079_assigned.fastq obiuniq -m sample pairedend_KD079_assigned.fastq > pairedend_KD079_assigned_uniq_new.fasta obiclean -s merged_sample -r 0.05 -H pairedend_KD079_assigned_uniq_new.fasta > pairedend_KD079_assigned_uniq_clean.fasta ecotag -R diat_embl127_taxon_good.fasta -d embl_127 pairedend_KD079_assigned_uniq_clean.fasta > pairedend_KD079_assigned_uniq_clean_embl127.fasta obitab -o pairedend_KD079_assigned_uniq_clean_embl127.fasta > pairedend_KD079_assigned_uniq_clean_embl127.txt