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Qiime2: Merging several DADA2 denoised run feature tables and representative sequences for Qiime version 2017.7
#!/bin/zsh
# Script for merging multiple DADA2 denoised Illumina runs
# Provide file "runs.list" containing list of runs
# File names has to be <run>_table.qza and <run>_rep-seqs.qza
# Written by Gisle Vestergaard
# Email: gisle@bio.ku.dk
zmodload zsh/mapfile
runs=( ${(f)mapfile[$PWD/runs.list]} )
for run in $runs;
if [ ! -f merged_rep-seqs.qza ];
then
scp "$run"_table.qza merged_table.qza
scp "$run"_rep-seqs.qza merged_rep-seqs.qza
else
qiime feature-table merge --i-table1 "$run"_table.qza --i-table2 merged_table.qza --o-merged-table merged_table.qza &
qiime feature-table merge-seq-data --i-data1 "$run"_rep-seqs.qza --i-data2 merged_rep-seqs.qza --o-merged-data merged_rep-seqs.qza
fi
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