CD-HIT: clustering FLYE against other assemblies

• Idea: To identify why FLYE is different or what is different
  • Concatenate all assemblies apart from flye
  • run cd-hit-est-2d between flye and "concatenated" assemblies
• Created a new branch cdhit from cleanup
• Commit IDs 3ccdb2ff 3e4b21c2 ecc1a4c5 4e48b4c2 b9936333

changed milestone to %Manuscript - initial version

added Analysis label

added Investigation label

changed the description

• cd-hit-est-2d fails when running from the conda version due to certain contigs being very long
• therefore using the binary from here: /work/projects/ecosystem_biology/local_tools_gaia/cd-hit-v4.6.1-2012-08-27_OpenMP_MAX_SEQ-5MBP/cd-hit-est-2d
• commit ID ecc1a4c5

assigned to @valentina.galata

TODO (maybe): incorporate into workflows?!

Closing because

• cdhit is run for all pairwise comparisons anyway
• current results suggest that all LR assemblies contain genes not found in other assemblies
  • low identity between some contigs (between assemblies)
• diamond or blast might be better

closed