TP2 de métagénomique, infection urinaire

wgs.sh 1.1KB

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  1. #!/bin/bash
  2. mkdir results
  3. # Question 1
  4. 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
  5. # Question 2
  6. # a
  7. samtools view -b results/alignment.sam
  8. # b
  9. samtools sort -@ 4 results/alignment.bam -o results/alignment.sorted.bam
  10. # c
  11. samtools index results/alignment.sorted.bam
  12. # d
  13. samtools idxstats -@ 4 results/alignment.sorted.bam > results/alignment.idx
  14. # f
  15. grep ">" databases/all_genome.fasta|cut -f 2 -d ">" > results/association.tsv
  16. # Question 3
  17. soft/megahit --k-list 21 --mem-flag 0 -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -o contigs
  18. # Question 4
  19. soft/prodigal -i contigs/final.contigs.fa -d results/genes.fna
  20. # Question 5
  21. sed "s:>:*\n>:g" results/genes.fna | sed -n "/partial=00/,/*/p"|grep -v "*" > results/genes_full.fna
  22. # Question 6
  23. 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
  24. # Les génomes présentent de nombreux gènes de résistances à des antibiotiques : catB7, floR, tet(A)....