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My Bioinformation Learning Page

基因组

组装

基因组注释

比较基因组

转录组

组装

  • Trinity
    Trinity assembles transcript sequences from Illumina RNA-Seq data.
  • megahit
    MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

注释

  • Diamond
    DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
  • interproscan 蛋白数据库uniprot,GO term注释,KEGG注释,pfam注释
  • ncbi nr
    nr,nt,swissprot数据库
  • eggNOG-mapper
    EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.

定量

差异表达

宏基因组&宏转录组

R相关脚本(from jianming zeng)

Contect me: [email protected]
Visit my github homepage here