Metagenomics Tools

Metagenomics.wiki

Sequence data analysis


 → 16S tools

  QIIME,  DADA2


→ Shotgun sequencing

  Alignment, QC, remove host sequence, ...


  → Assembly

  MEGAHIT, ...


 → BLAST

  Blast format, E-value, FastANI, ...


 → Bowtie2

  Reference database & mapping, ...


 → SAMtools

  Coverage, consensus, SAM format, ...


 → Ubuntu / Linux server

  gzip,  tar.gz,  sed,  awk,  shell loop,  ...


 → HPC SGE cluster

  qsub,  qstat,  qhost,  ...