igblast

conda  create -n repe -y  python=2
source activate repe
conda install -y igblast flash 
conda install -c bioconda seqkit 
for i in `seq -w 7 10`;
do prefetch ERR34450${i} \ done
for i in `seq -w 7 10`;
fastq-dump -A ERR34450${i}  -O ../raw --gzip --split-e ../ERR34450${i} | trim_galore -q 25 --phred33 --length 36 --stringency 3 --paired -o clean ERR34450${i}_1.fastq.gz ERR34450${i}_2.fastq.gz 
for i in `seq -w 7 10`;
flash ERR34450${i}_val_1.fastq.gz  ERR34450${i}_val_2.fastq.gz  -M 250 -o ./flash/ERR34450${i}; done
for i in `seq -w 7 10`; do seqkit fq2fa ERR34450${i}.extendedFrags.fastq > ERR34450${i}.fa; done