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