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- ANGSD
- BamTools
- Bartender
- BayeScan
- BayesTraits
- bgc
- BLAST
- BLAT
- Bowtie
- Bowtie2
- BWA
- Cactus
- Canu
- Exonerate
- eXpress
- Fastqc
- FASTX-Toolkit
- FreeBayes
- GATK
- GMAP
- Guppy
- Hal
- HISAT2
- JELLYFISH
- kallisto
- MaSuRCA
- Miniasm
- Minimap2
- NGMLR
- NGS Tools
- PAML
- PEAR
- PHAST
- Picard
- Pilon
- Porechop
- RELION
- RSEM
- Salmon
- SAM Tools
- SnpEff
- Stacks
- STAR
- Subread
- tabix
- trimmomatic
- Trinity
- VCFTools
...