These documents refer to an obsolete way of installing and running FALCON. They will remain up for historical context and for individuals still using the older version of FALCON/FALCON_unzip.


The current PacBio Assembly suite documentation which includes new bioconda instructions for installing FALCON, FALCON_unzip and their associated dependencies can be found here pb_assembly




FALCON Updates:

Repeat Masking

  • Integration of DAMASKER: Tandem repeat masking (done) and general repeat masking (in progress)

Improved default settings for microbial assembly

  • Use one longest read per ZMW: reduced chimerism, coverage bias
  • Retuned parameters to increase contiguity

New! GFA-2 support

  • Assembly graphs now written in both GFA-1 and GFA-2 formats
  • Placement coordinates of associate contigs now available in a new “contig.gfa2” file

Performance Improvements

  • General workflow and resource specification improvements
  • Easier integration of future features with Pbsmrtpipe

FALCON-Unzip Updates:

Improved Haplotig Extraction

  • Algorithm and data structure improvements reduce haplotype switching and improve extraction (resolved nested and overlapping haplotigs)
  • Can now handle circular contigs!

New! Placement Files

  • Haplotig placement (PAF format) generated after Unzip
  • Easier integration with FALCON-Phase

Performance Improvements

  • Use of Minimap2 instead of BLASR for phasing in Unzip reduces time requirements
  • Significantly reduced memory consumption of the final stage of Unzip (preads no longer have to be loaded in memory)
  • Unzipping and polishing are now combined in the same workflow and run consecutively.