Qiita plugin to process PacBio reads; it currently provides 2 commands for Qiita:

• Woltka v0.1.7, minimap2: which generates feature and functional profiles agains WoLr2; the expected output are BIOM artifacts
• PacBio processing: which goes from step 1 to 7 in the image below. The expected output is a main folder with folders per-sample and folders for each of the different outputs, as follows:
  • MAG folder: all Metagenome-Assembled Genome (MAG) generatedfor that sample
  • LCG folder: all Long-Circular Genome (LCG) generated for that sample that are over 512kb in size - approximate 515,000 bases (half a million)
  • small_LCG folder: all Long-Circular Genome (LCG) generated for that sample that are under 512kb in size
  • [sample-name].fna.gz: the no LCG reads used for MAG generation
  • [sample-name].checkm.txt.gz: MAG quanlity information from CheckM v1.2.3