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doit08-medaka.bash
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doit08-medaka.bash
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#! /bin/bash
. $(dirname ${BASH_SOURCE[0]})/doit-preamble.bash
# ------------------------------------------------------------------------
# Run Medaka to polish the consensus assembly
# (https://github.com/rrwick/Trycycler/wiki/Polishing-after-Trycycler)
# ------------------------------------------------------------------------
rm -rf ${MEDAKA}
mkdir ${MEDAKA}
echo 1>&2 '# Polishing with long reads (Medaka)'
for cluster_dir in ${RECONCILED}/cluster_[0-9]* ; do
cluster_name=$(basename $cluster_dir)
echo 1>&2 '##' $(basename $cluster_dir)
medaka_consensus \
-i ${cluster_dir}/4_reads.fastq \
-d ${cluster_dir}/7_final_consensus.fasta \
-o ${MEDAKA}/${cluster_name} \
-m r941_min_high_g360
done
cat ${MEDAKA}/cluster_*/consensus.fasta > ${MEDAKA}/polished.fasta
# ------------------------------------------------------------------------
# Done.
# ------------------------------------------------------------------------
echo 1>&2 ''
echo 1>&2 '# Done.'