perl wget perl-net-ssleay seqkit parallel entrez-direct minimap2 bwa htslib bowtie2 emboss bedtools samtools==1.10 bamtools sra-tools cutadapt seqtk datamash bcftools freebayes subread bioawk hisat2 bbmap trimmomatic fastqc snpeff picard blast vt readseq ucsc-bedgraphtobigwig cd-hit biopython==1.76 pysam ensembl-vep==101.0 trim-galore ucsc-liftover