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run_exp_basecall_analysis_guppy.sh
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run_exp_basecall_analysis_guppy.sh
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#!/bin/bash
ROOTDIR=$WORKINGDIR/data/Klebsiella_pneumoniae_INF032/
FASTA_FILE=$ROOTDIR/"Klebsiella_pneumoniae_INF032_reference.fasta"
# set following based on guppy mode
EXPDIR=$ROOTDIR/experiments/guppy_hac/
#EXPDIR=$ROOTDIR/experiments/guppy_fast/
BASECALLDIR=$EXPDIR/basecalled_fastq/
# set following based on guppy mode
GUPPY_CONFIG="dna_r9.4.1_450bps_hac.cfg"
#GUPPY_CONFIG="dna_r9.4.1_450bps_fast.cfg"
#GUPPY_CONFIG="dna_r10.3_450bps_hac.cfg"
#GUPPY_CONFIG="dna_r10.3_450bps_fast.cfg"
mkdir -p $BASECALLDIR
# basecalling
./basecall_guppy.sh $ROOTDIR/fast5 $BASECALLDIR/lossless.fastq $GUPPY_CONFIG
for i in {1..10}; do
./basecall_guppy.sh $ROOTDIR/experiments/new_fast5/LFZip_maxerror_$i $BASECALLDIR/LFZip_maxerror_$i.fastq $GUPPY_CONFIG
./basecall_guppy.sh $ROOTDIR/experiments/new_fast5/SZ_maxerror_$i $BASECALLDIR/SZ_maxerror_$i.fastq $GUPPY_CONFIG
done
# basecalling analysis
./analysis_basecall_accuracy.sh $BASECALLDIR/lossless.fastq $FASTA_FILE
for i in {1..10}; do
./analysis_basecall_accuracy.sh $BASECALLDIR/LFZip_maxerror_$i.fastq $FASTA_FILE
./analysis_basecall_accuracy.sh $BASECALLDIR/SZ_maxerror_$i.fastq $FASTA_FILE
done