usage: utgcns [opts]
INPUT
-G g Load reads from gkStore 'g'
-T t v p Load unitigs from tgStore 't', version 'v', partition 'p'.
Expects reads will be in gkStore partition 'p' as well
Use p='.' to specify no partition
-t file Test the computation of the unitig layout in 'file'
'file' can be from:
'tgStoreDump -d layout' (human readable layout format)
'utgcns -L' (human readable layout format)
'utgcns -O' (binary multialignment format)
-p package Load unitig and read from 'package' created with -P. This
is usually used by developers.
ALGORITHM
-quick No alignments, just paste read sequence into the unitig positions.
This is very fast, but the consensus sequence is formed from a mosaic
of read sequences, and there can be large indel. This is useful for
checking intermediate assembly structure by mapping to reference, or
possibly for use as input to a polishing step.
-pbdagcon Use pbdagcon (https://github.com/PacificBiosciences/pbdagcon).
This is fast and robust. It is the default algorithm. It does not
generate a final multialignment output (the -v option will not show
anything useful).
-utgcns Use utgcns (the original Celera Assembler consensus algorithm)
This isn't as fast, isn't as robust, but does generate a final multialign
output.
OUTPUT
-O results Write computed tigs to binary output file 'results'
-L layouts Write computed tigs to layout output file 'layouts'
-A fasta Write computed tigs to fasta output file 'fasta'
-Q fastq Write computed tigs to fastq output file 'fastq'
-P package Create a copy of the inputs needed to compute the unitigs. This
file can then be sent to the developers for debugging. The unitig(s)
are not processed and no other outputs are created. Ideally,
only one unitig is selected (-u, below).
TIG SELECTION (if -T input is used)
-u b Compute only unitig ID 'b' (must be in the correct partition!)
-u b-e Compute only unitigs from ID 'b' to ID 'e'
-f Recompute unitigs that already have a multialignment
-maxlength l Do not compute consensus for unitigs longer than l bases.
PARAMETERS
-e e Expect alignments at up to fraction e error
-em m Don't ever allow alignments more than fraction m error
-l l Expect alignments of at least l bases
-maxcoverage c Use non-contained reads and the longest contained reads, up to
C coverage, for consensus generation. The default is 0, and will
use all reads.
LOGGING
-v Show multialigns.
-V Enable debugging option 'verbosemultialign'.
ERROR: No gkpStore (-G) and no package (-p) supplied.
ERROR: No tigStore (-T) OR no test unitig (-t) OR no package (-p) supplied.