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Bartender is a c++ tool that is designed to process random barcode data. Bartender is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.

It currently has three functionalities.

  • It extracts barcodes from FASTA or FASTQ files.
  • It clusters barcode reads and counts the frequency of each cluster.
  • It generates count trajectories for time-course data.
Versionmodule name
1.1bartender/1.1
Example: /share/Apps/examples/bartender 
#!/bin/bash

#SBATCH -p lts
#SBATCH -t 60
#SBATCH -n 1
#SBATCH -N 5

module load bartender

cd /share/Apps/examples/bartender

bartender_single_com -f random_small_data/2M_extracted_barcode.txt -o 2M_barcode -d 3

bartender_single_com -f random_small_data/2M_extracted_barcode_umi.txt -o 2M_barcodei_umi -d 3

bartender_extractor_com -f random_small_data/2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2 -d both

bartender_extractor_com -f random_small_data/2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2 --direction=forward -u 0,10

echo "Deleting Files created"
rm -rf 2Mbarcode*

cd simulation_data

echo "This example requires 26GB RAM"

tar -xvzf simulated_data.tar.gz

bash clustering_test.sh
echo "Deleting Files created"
rm -rf cluster_result_new_barcode.csv  cluster_result_new_cluster.csv  cluster_result_new_quality.csv simulation_data.csv


For more information visit https://github.com/LaoZZZZZ/bartender-1.1

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