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merging_assemblies.md

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Quickmerge

We used Quickmerge to merge Supernova assembly into Flye assembly. Flye assembly had better completeness and contiguity so it was used as a primery assembly during merging. To do so, we used merge_wrapper script from quickmerge with -l value equals to the N50 value of Supernova assembly i.e 30358 and other parameters as in the script below.

Script for quickmerge

#!/bin/bash -e

#SBATCH --nodes 1
#SBATCH --cpus-per-task 1
#SBATCH --ntasks 10
#SBATCH --partition=large
#SBATCH --job-name quickmerge.ew
#SBATCH --mem=50G
#SBATCH --time=24:00:00
#SBATCH --account=uoo02752
#SBATCH --output=%x_%j.out
#SBATCH --error=%x_%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=bhaup057@student.otago.ac.nz
#SBATCH --hint=nomultithread

export PATH=/nesi/nobackup/uoo02752/bin/quickmerge:/nesi/nobackup/uoo02752/bin/quickmerge/MUMmer3.23:$PATH

merge_wrapper.py assembly.fasta EW_10xSN.fasta \
                  -hco 5.0 -c 1.5 -l 30358 -ml 5000 -p EW_Flye_SN_merge