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

Running Unzip on HGAP4 output


HGAP4 is a FALCON-based assembly pipeline, available through the SMRT Link interface. The pipeline itself encapsulates de novo assembly and polishing of the resulting contigs, but not the FALCON-unzip process as well. FALCON-unzip is currently available as a standalone tool, runnable only via command line.

Although HGAP4 runs FALCON under the hood, the folder structure it generates is different than that of FALCON. The FALCON-unzip, however, requires the assembly folders to be formatted in the FALCON-style.

This tutorial describes the necessary steps required to adjust the HGAP4 output to be compatible with a form required by FALCON-unzip.

In brief, the majority of work required to adjust the HGAP4 output to a FALCON-compatible directory structure is implemented in a script called hgap4_adapt. This script lives in the FALCON repository.

The complete process is composed of the following steps:

  1. Installing FALCON and FALCON-unzip.
  2. Running hgap4_adapt.
  3. Creating the fc_unzip.cfg configuration file for FALCON-unzip.
  4. Creating the input.fofn and input_bam.fofn.
  5. Running FALCON-unzip.

IMPORTANT: FALCON-unzip can only be run on HGAP4 jobs which had the Save Output for Unzip option turned on. It is not possible to run FALCON-unzip otherwise, because critical files will be missing from your job’s output.

1. Installing FALCON and FALCON-unzip

The latest versions of FALCON and FALCON-unzip are available as precompiled Linux binaries. The easiest approach to installing them is through a wrapper script, described here:

Quick Start

Follow this approach to set-up the environment before moving on to step 2.

Alternatively, one can install the binaries manually by following the instructions here:

2. Running hgap4_adapt

Once the FALCON installation was successful, one needs to activate the installation environment to make the hgap4_adapt script available. This will also activate FALCON and FALCON-unzip. To verify the installation, run the following:

source /path/to/your/install/dir/fc_env/bin/activate
python -m falcon_kit.mains.hgap4_adapt --help

If everything was successful, this should output verbose usage information to screen. After this is set-up and working, adapting an existing HGAP4 run is as simple as the following example (take note of the dummy path, and replace it with a real one):

source /path/to/your/install/dir/fc_env/bin/activate

mkdir –p example1
cd example1
python -m falcon_kit.mains.hgap4_adapt --job-output-dir=${job_dir}

The result should be visible in the example1 directory - it should now be populated to folders resembling a typical FALCON assembly run.

3. Creating the fc_unzip.cfg configuration file for FALCON-unzip

For help on .cfg files, please take a look at these Wiki pages:

4. Creating the input.fofn and input_bam.fofn

The input.fofn file (“file of file names”) contains the paths to files containing plain FASTA sequences of your raw reads, one file per row. All raw reads in the FASTA format should be available in your job dir:

mkdir –p example1
cd example1

echo "${job_dir}/tasks/pbcoretools.tasks.gather_fasta-1/file.fasta" > input.fofn

The input_bam.fofn is required for the polishing step. This file is composed of a list of all BAM files from the input dataset which was provided to the initial HGAP4 run:

source /path/to/your/install/dir/fc_env/bin/activate

mkdir –p example1
cd example1

dataset summarize ${job_dir}/tasks/pbcoretools.tasks.filterdataset-0/filtered.subreadset.xml | grep -E "*.bam$" > input_bam.fofn

5. Running FALCON-unzip

Before running FALCON-unzip, the adapted folder structure should be similar to the following:

$ cd example1
$ ls | xargs -n 1

Finally, to run FALCON-unzip, do the following:

source /path/to/your/install/dir/fc_env/bin/activate
cd example1 fc_unzip.cfg fc_unzip.cfg