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commands.txt
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commands.txt
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#CREATING READS WITH WGSIM
wgsim -e 0.05 -N 33950369 GCF_000005845_2_ASM584v2_genomic_fna 512_5_1.fq 512_5_2.fq
#MEGAHIT v.1.0.3
#INSTALLING
wget https://github.com/voutcn/megahit/releases/download/v1.0.3/megahit_v1.0.3_LINUX_CUDA6.5_sm350_x86_64-bin.tar.gz
tar zvxf megahit_v1.0.3_LINUX_CUDA6.5_sm350_x86_64-bin.tar.gz
#SPLITTING FILES FOR ASSEMBLER
split -l 530472 4_5_1.fq
mv xaa 2_5_1.fq
split -l 530472 4_5_2.fq
mv xaa 2_5_2.fq
#ASSEMBLY
megahit_v1.0.3_LINUX_CUDA6.5_sm350_x86_64-bin/megahit -1 2_5_1.fq -2 2_5_2.fq -o out_5err_2
#MEGAHIT v.1.1.12
#INSTALLING
conda install -c bioconda megahit=1.1.2
#SPLITTING FILES
split -l 530474 4_2_1.fq
#ASSEMBLY
megahit -1 2_0_1.fq -2 2_0_2.fq -o out -m 0.6
#CONVERTING CONTIGS TO .FASTG FORMAT FOR BANDAGE VISUALISATION
megahit_toolkit contig2fastg 41 k41_2.contigs.fa > k41_2.fastg
megahit_toolkit contig2fastg 41 k41_32.contigs.fa > k41_32.fastg
megahit_toolkit contig2fastg 41 k39_512.contigs.fa > k39_512.fastg
#mmetaSPAdes3.12.0
#INSTALLATION
wget http://cab.spbu.ru/files/release3.12.0/SPAdes-3.12.0-Linux.tar.gz
tar -xzf SPAdes-3.12.0-Linux.tar.gz
#SPLITTING FILES
split -n 2 512_0_1.fq
#ASSEMBLY
python3 metaspades.py --phred-offset 33 -1 2_5_1.fq -2 2_5_2.fq -o out
#QUAST
python quast.py -r ../cococoli.fna ../final.contigs*