Bartender

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.

This package is built using SPACK and optimized for AVX, AVX2 and AVX512 CPUs. To use the optimized version, you need to add source /etc/profile.d/zlmod.sh to your submit script before loading any modules. By default, the AVX2 optimized version (head node is Haswell CPU) is in your path. The AVX2 optimized version will run on Skylake (enge, im2080, chem, health) and Cascade Lake (hawkcpu, hawkmem, hawkgpu, infolab) CPUs but not on Ivybridge (debug) CPUs.

Version	module name
1.1	bartender/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