All the Conda Environments

• conda create -n fastqc -c bioconda fastqc
  FastQC is a quality control tool for high-throughput sequencing data.
• conda create -n trim-galore -c bioconda trim-galore
  Trim Galore is a wrapper tool for quality and adapter trimming of FASTQ files. Trimmomatic is a common alternative.
• conda create -n bwa -c bioconda bwa
  BWA (Burrows-Wheeler Aligner) is a fast and efficient tool for aligning sequencing reads to a reference genome. Bowtie2 is a common alternative.
• conda create -n samtools -c bioconda samtools
  Samtools is a suite of programs for manipulating high-throughput sequencing data in SAM/BAM/CRAM formats.
• conda create -n gatk4 -c bioconda gatk4
  GATK4 (Genome Analysis Toolkit v4) is a powerful toolkit for variant discovery in high-throughput sequencing data.
• conda create -n qualimap -c bioconda qualimap
  Qualimap is a tool for evaluating the quality of sequencing alignment data.
• conda create -n bcftools -c bioconda bcftools
  BCFtools is a set of utilities for processing and analyzing VCF and BCF files.
• conda create -n vcftools -c bioconda vcftools
  VCFtools is a program suite for working with VCF files, enabling filtering and summarizing.
• conda create -n r_env -c conda-forge r-base r-ggplot2 r-scales
  Creates a Conda environment named r_env with R, ggplot2, and scales packages from conda-forge.
• conda create -n plink -c bioconda plink
  PLINK is a toolset for whole-genome association studies.
• conda create -n strelka -c bioconda strelka
  Strelka is a high-performance variant calling tool for small variants in next-generation sequencing data.
• conda create -n admixture -c bioconda admixture
  Admixture is a tool used to estimate ancestries from genotype datasets.
• conda create -n rtg-tools -c bioconda rtg-tools
  RTG Tools is a software suite used to compare VCF files, generate variant statistics, and benchmark variant calling pipelines.