BWA (v0.7.17-r1188)
Samtools (v1.10)
GATK (v4.1.8.1)
BLAST+ (v1.12.0+)
Clustal Omega (v1.2.4)
FLASH (v1.2.11)
trimmomatic (v0.38)

download blast database: https://ftp.ncbi.nih.gov/blast/db/FASTA/
bulid blastdb: "makeblastdb -dbtype nucl -in ntdatabase -input_type fasta -out nt.blastdb -parse_seqids"

note: raw nt database contain 'N' characters, please remove it before using 'makeblastdb' command bulid blast database

conda create -n cleanSeq python==3.8
conda activate cleanSeq
conda install -c conda-forge biopython (v:1.79)
conda install -c anaconda pandas (v:1.1.3)
conda install -c anaconda reportlab (v:3.5.51)
conda install -c conda-forge bs4 (v:4.10.0)
conda install -c anaconda requests (v:2.24.0)
conda install -c anaconda openpyxl (v:3.0.5)
conda install -c conda-forge matplotlib (v:3.2.2)
conda install -c anaconda xlrd (v:1.79)

command: chmod a+x ./cleanSeq
         ./cleanSeq reference.fa raw1.fq.gz raw2.fq.gz ntPath

command: cleanSeq command: python cleanSeq.py reference.fa raw1.fq.gz raw2.fq.gz ntPath