My Bioinformation Learning Page

基因组

组装

• pacbio测序基因组组装软件CANU
• 三代测序组装软件FALCON
• 基因组修剪打磨NextPolish

基因组注释

比较基因组

• 短片段比较bwa
• 大片段比较LASTZ
• 适用多平台测序结果大片段比对minimap2

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

• RSEM

差异表达

• 有重复DESeq
• 无重复edgeR

宏基因组&宏转录组

• QIIME2

R相关脚本(from jianming zeng)

• R

Contect me: wangjingtian@stu.xmu.edu.cn
Visit my github homepage here