42 lines
1.1 KiB
Bash
42 lines
1.1 KiB
Bash
#!/bin/bash
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mkdir results
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# Question 1
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soft/bowtie2 --end-to-end --fast -x databases/all_genome.fasta -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -S results/alignment.sam
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# Question 2
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# a
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samtools view -b results/alignment.sam
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# b
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samtools sort -@ 4 results/alignment.bam -o results/alignment.sorted.bam
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# c
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samtools index results/alignment.sorted.bam
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# d
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samtools idxstats -@ 4 results/alignment.sorted.bam > results/alignment.idx
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# f
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grep ">" databases/all_genome.fasta|cut -f 2 -d ">" > results/association.tsv
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# Question 3
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soft/megahit --k-list 21 --mem-flag 0 -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -o contigs
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# Question 4
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soft/prodigal -i contigs/final.contigs.fa -d results/genes.fna
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# Question 5
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sed "s:>:*\n>:g" results/genes.fna | sed -n "/partial=00/,/*/p"|grep -v "*" > results/genes_full.fna
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# Question 6
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blastn -query results/genes_full.fna -db databases/resfinder.fna -perc_identity 0.8 -qcov_hsp_perc 0.8 -evalue 1e-3 -outfmt 6 -out results/annoted_genes.dat
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# Les génomes présentent de nombreux gènes de résistances à des antibiotiques : catB7, floR, tet(A)....
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