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abysscutadaptpicardvcftools
bamtoolsfasta3raxmlmultiqc
bbmapfastqcsamtools
bcftoolsgatk4spades
bedtoolshisat2star
blasthtseqstringtie
bowtieigvtabix
bowtie2jbrowsetcoffee
bwamantatophat
cufflinksmrbayestrimmomatic
R

bioconductor

deseq2
edgeR
ballgown
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