pbjd/pbutgcns

DAG-based consensus caller for celera assemblers unitigs

pbutgcns

DAG-based consensus caller for celera assemblers unitigs. It is currently
tested only using pacbio corrected reads, though in prinicipal it could be
used for pacbio un-corrected. It currently uses a simple python adapter
to interface with the tigStore. Eventually, this is expected to be replaced
with a more direct call to lower-level API calls.

Building

> make BLASR=<path to blasr>
> ./pbutgcns -h

Support libraries needed

• pblibblasr BLASR library
• boost Popular C++ utility library (1.46 or 1.47)
• log4cpp Logging library (1.0 or 1.1)

Running

The input is an assembly generated by celera-assembler, typically only through
the unitigger stage. However, if you want to compare it to the existing consensus
caller, it can be run to completion. Either one will work.

A utitilty shell script pbutgcns_wf.sh can be used to execute the consensus
workflow for a given file containing a list of unitigs ids. Make sure that you
have CA's tigStore and gatekeeper utilities, tigStore-adapter.py and pbutgcns
in your path.

# tmp: temporary directory to generate consensus into
# cap: CA-prefix used in celera assembler
# nproc: number of threads to use while building consensus
# cns: the output file name
> tmp=/tmp cap=asm utg=utg.lst nproc=4 cns=utg_consensus.fa pbutgcns_wf.sh