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| # Packages available in the Homebrew and Linuxbrew package manager | |
| --- | |
| bio_nextgen: | |
| alignment: | |
| - bwa | |
| - bowtie2 | |
| - novoalign | |
| - rna-star | |
| utilities: | |
| - bamtools | |
| - bedtools | |
| - cramtools | |
| - biobambam | |
| - fastqc | |
| - fastx_toolkit | |
| - qualimap | |
| - sambamba-binary | |
| - staden_io_lib | |
| analysis: | |
| - cufflinks-binary | |
| - samtools | |
| - htslib | |
| - bcftools | |
| #- tophat | |
| variant: | |
| - delly;--with-binary | |
| - freebayes | |
| - gatk-framework | |
| - lofreq | |
| - lumpy-sv | |
| - pindel | |
| - platypus-variant | |
| - rtg-tools | |
| - scalpel | |
| - snpeff | |
| - theta2 | |
| - vardict | |
| - vcflib | |
| - vcftools | |
| - vep | |
| - wham | |
| # - yaha The Principal Investigator has moved; the software does not download ATM | |
| integration: | |
| - biointerchange | |
| distributed: | |
| - parallel |