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 Assembler


associated contig
Alternate configuration (phase) of a portion of a primary contig*. See this discussion on primary vs associated contigs
compound path
multi-paths from a single source to a single sink in a graph
contiguous sequence output from a genome assembler
error correction
The process of combining data from multiple raw sequences with random error profile together to eliminate the errors.
full-pass subread
A subread that begins at one adapter sequence and ends at another adapter sequence. A full-pass subread does not begin or end in the middle of an insert sequence.
Contig from specific haplotype
Pre-assembled Reads, error corrected reads through the pre-assembly process.
Error correction process assembling raw sequences to generate high qualityy consensus for the final step of assembly.
primary contig
contig which captures a contiguous part of a genome regardless the variations due to the variation between haplotypes associated contig generated by alternative paths from a portion in the primary contig
proper overlap
read overlaps without unaligned overhangs:
A highly accurate consensus and variant caller that can generate 99.999% accurate consensus sequences using local realignment and the full range of quality scores associated with Pacific Biosciences reads. Part of the SMRT® Analysis suite.
Uncorrected raw SMRTcell movie data
simple path
a path without any branches in the assembly graph
string graph
see The fragment assembly string graph by Eugene W. Myers, 2005
Each polymerase read is partitioned to form one or more subreads, which contain sequence from a single pass of a polymerase on a single strand of an insert within a SMRTbell™ template and no adapter sequences. The subreads contain the full set of quality values and kinetic measurements. Subreads are useful for applications like de novo assembly, resequencing, base modification analysis, and so on.