忘備録として
CONDA
https://conda.io/docs/index.html
BIOCONDA
パッケージマネージャー。ソフトウェアのインストール、バージョン管理、パス設定など。
BWA
http://bio-bwa.sourceforge.net/
マッピング
SAMtools
https://github.com/samtools/samtools
"Various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format"
freebayes
https://github.com/ekg/freebayes
"Bayesian haplotype-based genetic polymorphism discovery and genotyping"
Genome Analysis Toolkit (GATK)
https://software.broadinstitute.org/gatk/
Stacks
http://catchenlab.life.illinois.edu/stacks/
"de novo map pipeline"
GBS SNP Calling Reference Optional Pipeline (GBS-SNP-CROP)
https://github.com/halelab/GBS-SNP-CROP
Mock referenceの作成によるSNP検出のPipeline. 勉強中
PLINK
https://www.cog-genomics.org/plink2
VCFtools
https://vcftools.github.io/index.html
STRUCTURE
http://web.stanford.edu/group/pritchardlab/structure.html
fastSTRUCTURE
https://rajanil.github.io/fastStructure/
Admixture
https://www.genetics.ucla.edu/software/admixture/index.html
pophelper
https://github.com/royfrancis/pophelper
STRUCTURE解析結果の出力に。自由度高く、distructより使いやすい。
DIYABC