45 lines
1.3 KiB
Bash
45 lines
1.3 KiB
Bash
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### Environment Setting
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DirRaw=00_raw
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DirQcTrim=01_fastp
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DirAssembly=02_spades
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### Get some arrays
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cd $DirRaw
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readarray -t full_names < <(ls | awk -F '_' '{print $1 "_" $2 "_" $3 "_" $4}' | uniq)
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readarray -t species_names < <(ls | awk -F '_' '{print $2 "_" $3}' | uniq)
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readarray -t output_names < <(ls | awk -F '_' '{print $2 "_" $3 "_" $4}' | uniq)
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cd ..
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length_fn=${#full_names[@]}
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length_sn=${#species_names[@]}
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length_on=${#output_names[@]}
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### Check the arrays
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if [ $length_fn -ne $length_sn ] || [ $length_fn -ne $length_on ] || [ $length_sn -ne $length_on ]
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then
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echo "Please check the amount number of arrays"
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exit 0
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fi
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### Quality control && Trimming
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mkdir -p $DirQcTrim
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for (( i=0; i<$length_fn; i++ )); do
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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
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done
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### De novo assembly
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mkdir -p $DirAssembly
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for (( i=0; i<$length_fn; i++ )); do
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mkdir -p $DirAssembly/${species_names[$i]}
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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]}
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done
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