FALCON-Unzip contains the modules that works with FALCON ( https://github.com/PacificBiosciences/FALCON, https://github.com/PacificBiosciences/FALCON-integrate) for full diploid assembly (representing haplotype specific contigs as "haplotigs" as assembly output). A manuscript is deposited in BioRxiv (http://biorxiv.org/content/early/2016/06/03/056887) for our evalution and showing the application of the algorithms and the software on multiple diploid genomes. You can find more information here: https://github.com/PacificBiosciences/FALCON/wiki/FALCON-FALCON-Unzip-%22For-Phased-Diploid-Genome-Assembly-with-Single-Molecule-Real-Time-Sequencing%22
Note that this is under continuous development work. We will be keeping improving the code and algorithm for more efficient computation and improvement on the accuracy of assembly results. We do plan to refactor the code soon for furture maintainance purposes. Currently, the code is in its infant stage. If you are not familiar with working source code directly, you might want to wait a bit for the package and intergration reach certain maturity to try it out.
See example/unzip.sh for end-to-end work. You do need to have run it in a working diretory with Falcon output and all original Daligner overlap data.
For generating quiver consensus, you will need PacBio raw sequence data with "signal pulse" information in bam format. You can config the bam-file input using a configuration sent to fc_quvier.py.
To use this code to generate draft haplotig assembly, it need Falcon (please install the latest code from https://github.com/PacificBiosciences/FALCON-integrate). It also use nucmer for aligning contigs to find redundant contigs. You should have it in your execution path.
For "quivering" the draft haplotigs, you will need PacBio SMRTanalysis Software suit. More specifically, you need the following executables:
samtools
pbalign
makePbi
variantCaller
You will also need extra a python package pysam.
J.C. Jun, 2016