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config_ovl_filter_opt --max-diff 80
--max-cov 100
--min-cov 2
--bestn 10
--min-len 4000
--gapFilt
--minDepth 4
--idt-stage2 98
Overlap filter options.
--gapFilt - Enables the chimera filter, which analyzes
each overlap pile, and determines whether a pread is
chimeric based on the local coverage across the pread.
--minDepth - Option for the chimera filter. The chimera
filter is ignored when a local region of a read has
coverage lower than this value.
The other parameters are:
--min-cov - Minimum allowed coverage at either the 5'
or the 3' end of a read. If the coverage is below this
value, the read is blacklisted and all of the overlaps it is
incident with are ignored. This helps remove potentially
chimeric reads.
--max-cov - Maximum allowed coverage at either the 5'
or the 3' end of a read. If the coverage is above this
value, the read is blacklisted and all of the overlaps it is
incident with are ignored. This helps remove repetitive
reads which can make tangles in the string graph. Note
that this value is a heuristic which works well for ~30x
seed length cutoff. If the cutoff is set higher, we advise
that this value be also increased. Alternatively, using the
autocompute_max_cov option can automatically
estimate the value of this parameter, which can improve
contiguity (for example, in cases when the input genome
size or the seed coverage were overestimated).
--max-diff - Maximum allowed difference between the
coverages at the 5' and 3' ends of any particular read. If
the coverage is above this value, the read is blacklisted
and all of the overlaps it is incident with are ignored. If the
autocompute_max_cov option is used, then the same
computed value is supplied to this parameter as well.
--bestn - Keep at most this many overlaps on the 5'
and the 3' side of any particular read.
--min-len - Filter overlaps where either A-read or the
B-read are shorter than this value.
--idt-stage2 - Filter overlaps with identity below 98%.
--high-copy-sample-rate - Controls the
downsampling of reads from high copy elements to the
expected coverage determined by maxCov*rate, where
rate is the value of this parameter. If rate is 0, then
these high coverage reads are discarded.
config_ovl_min_idt 98 The final overlap identity threshold. Applied during the
final filtering stage, right before the overlaps are passed
to the layout stage.
config_ovl_min_len 1000 The minimum length of either A-read or a B-read to keep
the overlap. Applied during the final filtering stage, right
before the overlaps are passed to the layout stage.
config_ovl_opt --one-hit-per-
target
--min-idt 96
Overlapping options for the pancake overlapping tool.
The options set by this parameter here are passed
directly to pancake. For details on pancake options,
use pancake -h.
The defaults used here are: --one-hit-per-target
which keeps only the best hit in case there are multiple
possible overlaps between a pair of reads (tandem
repeats); and --min-idt 96 which will filter out any
overlap with identity lower than 96%.
config_phasing_opt
NONE Options for the phasing tool nighthawk. The options
set by this parameter are passed directly to nighthawk.
For details on nighthawk options, use nighthawk -h.
Advanced parameters Default value Description