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script_assembly_megahit.sh
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script_assembly_megahit.sh
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#!/bin/sh
## BY FATIMA-ZAHRA ABANI
#SBATCH --job-name=megahit_match
#SBATCH --mail-user fatima-zahra.abani@cirad.fr
#SBATCH --partition=long
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=50G
#Importation des modules
module load megahit/1.2.9
# Assemblage par megahit
megahit -1 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-o output_megahit_tri
#Importation du module
module load cap3-10.2011
#lancer cap3
cap3 final.contigs.fa
#importer quast
module load quast/5.0.2
#Analyse des résultats de metaspades avec quast
quast.py -o quast_results final.contigs.fa
# Chargement du module Diamond
module load diamond
diamond blastx -b 10.0 -c 1 -p 16 -d /shared/ifbstor1/bank/nr/current/diamond/nr --taxonmap prot.accession2taxid.gz --more-sensitive --query final_contigs_cap3_concat.fa --max-hsps 1 --max-target-seqs 5 -f 6 qseqid sseqid qlen slen length qstart qend sstart send qcovhsp pident evalue bitscore staxids --out result_diamond_cap3.tsv
#Extaction de la colonne 14 (Tax-Id)
cut -f 14 result_diamond.tsv | sort | uniq > tax_id.txt
#Téléchargement de l'ensemble de fichiers contenant les informations taxonomiques de la base de données de taxonomie du NCBI.
mkdir taxonomie
cd taxonomie
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -zxvf taxdump.tar.gz
cp names.dmp nodes.dmp delnodes.dmp merged.dmp ~/.taxonkit
#Commande de création d'un fichier tsv qui va contenir la taxonomie des taxid donnés par diamond
echo -e "taxid\trank\tname\tlineage\tkingdom\tphylum\tclass\torder\tfamily\tgenus\tspecies\tstrain" > taxonkit_megahit.tsv ; cat tax_id.txt | ./taxonkit reformat -I 1 -r "Unassigned" -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}\t{t}" >> taxonkit_megahit.tsv