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

pbutgcns's Issues

License Clarification

Hi, I am looking to either package this for Debian or include it with the package under preparation for the Celera Assembler (since it seems to be the only program that uses this). In either case, the missing license terms are problematic for Debian. Would you clarify it in the source distribution?