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alignment assembly atac-seq bam bash bbduk bbmap bbtools bioanalyzer bioinfomatics bioinformactics bioinformatics bowtie bowtie2 bwa cancer chip-seq coverage cuffdiff cufflinks demultiplexing deseq deseq2 dna-seq epigenetics error fasta fastq ffpe gatk genetics genome genomics hisat2 htseq-count illumina index linux mapping metagenomics methylation microbiome minion miseq na12878 nextera nextseq ngs novaseq pacbio programming python qiagen reads rna rna-seq rnaseq rrbs samtools sequencing snp software statistics tophat trimmomatic truseq vcf velvet wgs workshop

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