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--- nanopore_tools_for_polishing [2022/07/12 10:20] – 134.190.232.29
+++ nanopore_tools_for_polishing [2024/08/07 13:01] (current) – 134.190.232.164
@@ Line 1: / Line 1: @@
 ====== Polishing your MinION assembly ======
 Documentation by Jon Jerlström Hultqvist and Shelby Williams
+(updates by Joran Martijn)
 **Be aware that some scripts and commands might not be working any longer on Perun due to the switch to the new conda-environment system. Sections will be progressively updated to reflect this.**
@@ Line 133: / Line 134: @@
 Shell script:
 {{ :unicyclersh.docx |}}
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -cwd
+#$ -pe threaded 16
+#cd /scratch2/jon/MinION/BMAN/assemblies/Unicycler_polish/
+echo "Starting"
+unset PYTHONPATH
+export PATH=/scratch2/software/gcc-6.3.0/bin:/scratch2/software/Python-3.6.0/bin:$PATH
+export LD_LIBRARY_PATH=/scratch2/software/gcc-6.3.0/lib64:/scratch2/software/Python-3.6.0/lib:$LD_LIBRARY_PATH
+/scratch2/software/Python-3.6.0/bin/unicycler_polish -1 /scratch2/shelbyw/RCL_Unicycler/RCL_1_PairNtrim.fq -2 /scratch2/shelbyw/RCL_Unicycler/RCL_2_PairNtrim.fq --long_reads RCL_MinION.CutAdapt75.3000.chop.fastq.gz -a RCL_unclean_AB_assembly_fix_Racon2_Pilon3.fasta --pilon=/scratch2/software/pilon/pilon-1.22.jar --samtools=/opt/perun/bin/samtools --threads 16
+echo "Done!"
+</code>
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