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abacas
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abricate
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adapterremoval
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adapterremovalfixprefix
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agrvate
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allelecounter
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ampir
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amplify/predict
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amps
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amrfinderplus
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angsd/docounts
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antismash
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ariba
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arriba
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artic
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ascat
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assemblyscan
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ataqv
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atlas
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bakta
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bamaligncleaner
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bamcmp
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bamtools
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bamutil/trimbam
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bandage/image
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bases2fastq
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bbmap
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bcftools
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bcl2fastq
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bclconvert
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bedtools
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biobambam
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biscuit
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bismark
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blast
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bowtie
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bowtie2
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bracken
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busco
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bwa
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bwamem2
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bwameth
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cat
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cellranger
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centrifuge
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checkm/lineagewf
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chromap
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clonalframeml
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cmseq/polymut
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cnvkit
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cnvpytor
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controlfreec
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cooler
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csvtk
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custom
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cutadapt
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damageprofiler
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dastool
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dedup
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deeparg
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deepbgc
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deeptools
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deepvariant
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delly/call
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diamond
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dragmap
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dragonflye
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dshbio
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ectyper
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eido
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elprep
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emboss/seqret
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emmtyper
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endorspy
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ensemblvep
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entrezdirect
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epang
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expansionhunter
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faqcs
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fargene
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fastani
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fastawindows
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fastk
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fastp
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fastqc
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fastqscan
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fasttree
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ffq
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fgbio
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filtlong
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flash
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flye
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fq/lint
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freebayes
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gamma/gamma
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gappa
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gatk
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gatk4
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gecco/run
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genescopefk
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genmap
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genmod
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genomescope2
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genotyphi/parse
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genrich
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gfaffix
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gffread
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glimpse/chunk
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glnexus
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goat/taxonsearch
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graphmap2
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gstama
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gtdbtk/classifywf
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gubbins
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gunc
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gunzip
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gvcftools/extractvariants
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hamronization
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haplocheck
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haplogrep2/classify
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happy
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hicap
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hifiasm
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hisat2
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hmmcopy
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hmmer
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hmtnote
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homer
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hpsuissero
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ichorcna
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idr
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imputeme/vcftoprs
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instrain/profile
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iqtree
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ismapper
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isoseq3
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ivar
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jupyternotebook
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kaiju
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kallisto/index
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kallistobustools
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kat/hist
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khmer
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kleborate
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kraken2/kraken2
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krakentools
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krona
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last
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leehom
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legsta
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lima
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lissero
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lofreq
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macrel/contigs
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macs2/callpeak
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mafft
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malt
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maltextract
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manta
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mapdamage2
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mash
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mashtree
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maxbin2
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maxquant/lfq
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mcroni
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md5sum
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medaka
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megahit
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megan
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meningotype
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merqury
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merquryfk
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meryl
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metabat2
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metaphlan3
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methyldackel
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minia
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miniasm
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minimap2
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mlst
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mobsuite/recon
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mosdepth
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motus
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msisensor
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msisensor2
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msisensorpro
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mtnucratio
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multiqc
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multivcfanalyzer
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mummer
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muscle
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mykrobe/predict
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nanolyse
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nanoplot
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ncbigenomedownload
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nextclade
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nextgenmap
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ngmaster
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ngscheckmate/ncm
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nucmer
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optitype
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pairix
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pairtools
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panaroo/run
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pangolin
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paraclu
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pasty
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pbbam/pbmerge
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pbccs
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pbptyper
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pear
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peddy
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phantompeakqualtools
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phyloflash
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picard
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pints/caller
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pirate
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plasmidfinder
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plasmidid
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plink
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plink2
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pmdtools/filter
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porechop
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preseq
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prinseqplusplus
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prodigal
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prokka
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pycoqc
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pydamage
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qcat
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qualimap
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quast
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racon
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rapidnj
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rasusa
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raven
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raxmlng
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rgi/main
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rhocall/annotate
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rmarkdownnotebook
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roary
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rsem
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rseqc
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rtgtools
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salmon
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samblaster
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samtools
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scoary
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scramble
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seacr/callpeak
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seqkit
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seqsero2
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seqtk
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sequenzautils
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seqwish/induce
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seroba/run
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sexdeterrmine
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shasum
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shigatyper
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shovill
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sistr
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slimfastq
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snapaligner
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snippy
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snpdists
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snpeff
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snpsift/split
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snpsites
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somalier
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sourmash/sketch
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spades
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spatyper
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sratools
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srst2/srst2
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ssuissero
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stadeniolib/scramble
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staphopiasccmec
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star
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stranger
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strelka
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stringtie
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subread/featurecounts
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svdb
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svtk/standardize
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tabix
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tailfindr
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tbprofiler/profile
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tiddit
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transdecoder
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trimgalore
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trimmomatic
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ucsc
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ultra
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umitools
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unicycler
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untar
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unzip
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vardictjava
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variantbam
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vcf2db
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vcf2maf
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vcfanno
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vcflib/vcfuniq
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vcftools
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vsearch
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whamg
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yara
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