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mash.sh
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#!/bin/bash
#Reference+denovo+Re-scaffolded with unmapped reads at 10Ns
referencebasedassembly=/projects/data/team1_genomeAssembly/reference_based_assembly/assembly_all
for a in $(cat /projects/home/nshah377/IDs.txt)
do
echo "$a"
mash sketch /projects/data/team1_genomeAssembly/reference_based_assembly/assembly_all/$a/ref_10_and_denovo.final.scaffolds.fasta \
-o /projects/data/team1_genomeAssembly/MASH/refdenovo/$a.refdenovo
done
#SKESA
referencebasedassembly=/projects/data/team1_genomeAssembly/reference_based_assembly/assembly_all
for a in $(cat /projects/home/nshah377/IDs.txt)
do
echo "$a"
mash sketch /projects/data/team1_genomeAssembly/denovo_skesa/sspaceOutput/$a.sspace.final.scaffolds.fasta \
-o /projects/data/team1_genomeAssembly/MASH/skesa/$a.skesa
done
#SPADES
for a in $(cat /projects/home/nshah377/IDs.txt)
do
for b in $(ls /projects/data/team1_genomeAssembly/transfer/$a/output/fasta)
do
echo "$a,$b"
mash sketch /projects/data/team1_genomeAssembly/transfer/$a/output/fasta/$b \
-o /projects/data/team1_genomeAssembly/MASH/spades/$a.$b
done
done