init

batch.sh

@@ -0,0 +1,44 @@
+### Environment Setting
+
+DirRaw=00_raw
+DirQcTrim=01_fastp
+DirAssembly=02_spades
+
+### Get some arrays
+
+cd $DirRaw
+
+readarray -t full_names < <(ls | awk -F '_' '{print $1 "_" $2 "_" $3 "_" $4}' | uniq)
+readarray -t species_names < <(ls | awk -F '_' '{print $2 "_" $3}' | uniq)
+readarray -t output_names < <(ls | awk -F '_' '{print $2 "_" $3 "_" $4}' | uniq)
+
+cd ..
+
+length_fn=${#full_names[@]}
+length_sn=${#species_names[@]}
+length_on=${#output_names[@]}
+
+### Check the arrays
+
+if [ $length_fn -ne $length_sn ] || [ $length_fn -ne $length_on ] || [ $length_sn -ne $length_on ]
+then
+  echo "Please check the amount number of arrays"
+  exit 0
+fi
+
+### Quality control && Trimming
+
+mkdir -p $DirQcTrim
+
+for (( i=0; i<$length_fn; i++ )); do
+	fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j ${species_names[$i]}.json -h ${species_names[$i]}.html -o $DirQcTrim/${output_names[$i]}_R1.fastq.gz -O $DirQcTrim/${output_names[$i]}_R2.fastq.gz -w 4
+done
+
+### De novo assembly
+
+mkdir -p $DirAssembly
+
+for (( i=0; i<$length_fn; i++ )); do
+	mkdir -p $DirAssembly/${species_names[$i]} 
+	spades.py --pe1-1 $DirQcTrim/${output_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${output_names[$i]}_R2.fastq.gz -t 8 -k 97,107,117,127 -m 14 --careful --phred-offset 33 -o $DirAssembly/${species_names[$i]}
+done