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7_SR_polishing.md

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Bonus 2

If you also have short-read Illumina data corresponding to your Nanopore data. Use the high-accuracy short-read data to polish your best long-read assembly again. Use Polypolish for that. Install Polypolish and familiarize yourself with the tool. For the necessary mapping of the short reads to the assembly you should use bwa. Check the Polypolish manual!

get data

Quick start

(see https://github.com/rrwick/Polypolish/wiki/How-to-run-Polypolish for more details!)

bwa index draft.fasta
bwa mem -t 16 -a draft.fasta reads_1.fastq.gz > alignments_1.sam
bwa mem -t 16 -a draft.fasta reads_2.fastq.gz > alignments_2.sam
polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam
polypolish draft.fasta filtered_1.sam filtered_2.sam > polished.fasta

Next: Assembly data analysis