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Contents
#!/bash
# An example OTU clustering pipeline
# Austin G. Davis-Richardson
# <harekrishna at gmail dot com>
# http://github.com/audy/lederhosen
set -e
raw_reads='spec/data/*.txt'
out_dir='pipeline'
taxcollector='taxcollector.fa'
min_reads=50
min_samples=10
# trim reads
lederhosen trim \
--reads-dir=$raw_reads \
--out-dir=$out_dir/trimmed
# join reads
lederhosen join \
--trimmed=$out_dir/trimmed/*.fasta \
--output=$out_dir/joined.fasta
# filter reads
lederhosen k_filter \
--input=$out_dir/joined.fasta \
--output=$out_dir/filtered.fasta \
-k=10 \
--cutoff=50
# sort
lederhosen sort \
--input=$out_dir/filtered.fasta \
--output=$out_dir/sorted.fasta
for i in 0.80 0.90 0.95
do
# cluster
lederhosen cluster \
--input=$out_dir/sorted.fasta \
--output=$out_dir/clusters_"$i".uc \
--identity=$i
# filter uc file
lederhosen uc_filter \
--input=$out_dir/clusters_"$i".uc \
--output=$out_dir/clusters_"$i".uc.filtered \
--reads=$min_reads \
--samples=$min_samples \
# generate otu table
lederhosen otu_table \
--clusters=$out_dir/clusters_"$i".uc.filtered \
--output=$out_dir/otus_"$i"
# get representative reads
lederhosen rep_reads \
--clusters=$out_dir/clusters_"$i".uc.filtered \
--joined=$out_dir/sorted.fasta \
--output=$out_dir/representatives_"$i".fasta
# blast representative reads
lederhosen name \
--reps=$out_dir/representatives_"$i".fasta \
--output=$out_dir/taxonomies_"$i".txt \
--database=$taxcollector
done
echo "complete!"
Version data entries
37 entries across 37 versions & 1 rubygems