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Bartender

Bartender converts sequence data to a frequency table containing discovered barcode and raw reads count.

Bartender is available as a module on Apocrita.

Usage

To run the latest installed version of Bartender, simply load the bartender module:

module load bartender

For usage documentation, run pass the -h switch to any of the Bartender python scripts, for example: bartender_combiner_com -h.

Example job

Serial job

Here is an example job running on 2 cores and 2GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load bartender

# Test extractor using example barcode pattern
bartender_extractor_com -f example.fq \
                        -o example \
                        -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA

# Group barcodes using the clustering component
bartender_single_com -f example_barcode.txt \
                     -o example \
                     -t ${NSLOTS}

Reference