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$ wfmash -h
wfmash [target] [queries...] {OPTIONS}
wfmash: base-accurate alignments using mashmap2 and the wavefront algorithm
OPTIONS:
-h, --help display this help menu
-t[N], --threads=[N] use this many threads during parallel
steps
target alignment target or reference sequence
file
-L[targets],
--target-file-list=[targets] alignment target file list
queries... query sequences
-Q[queries],
--query-file-list=[queries] alignment query file list
-s[N], --segment-length=[N] segment length for mapping (1k = 1000,
1m = 10^6, 1g = 10^9) [default: 5000]
-l[N], --block-length-min=[N] keep mappings with at least this block
length (1k = 1000, 1m = 10^6, 1g = 10^9)
[default: 3*segment-length]
-k[N], --kmer=[N] kmer size <= 16 [default: 16]
-N, --no-split disable splitting of input sequences
during mapping [enabled by default]
-p[%], --map-pct-id=[%] use this percent identity in the mashmap
step [default: 95]
-K, --keep-low-map-id keep mappings with estimated identity
below --map-pct-id=%
-O, --keep-low-align-id keep alignments with gap-compressed
identity below --map-pct-id=%
-f, --no-filter disable mapping filtering
-n[N],
--num-mappings-for-segment=[N] number of mappings to retain for each
segment [default: 1]
-S[N],
--num-mappings-for-short-seq=[N] number of mappings to retain for each
sequence shorter than segment length
[default: 1]
-X, --skip-self skip self mappings when the query and
target name is the same (for all-vs-all
mode)
-Y[C], --skip-prefix=[C] skip mappings when the query and target
have the same prefix before the given
character C
-m, --approx-map skip base-level alignment, producing an
approximate mapping in PAF
-M, --no-merge don't merge consecutive segment-level
mappings
-w[N], --window-size=[N] window size for sketching. If 0, it
computes the best window size applying 0
as p-value cutoff [default:
automatically computed applying 1e-120
as p-value cutoff]
-e[spaced-seed],
--spaced-seed=[spaced-seed] Params to generate spaced seeds
<weight_of_seed> <number_of_seeds>
<similarity> <region_length> e.g "10 5
0.75 20"
-i[FILE], --input-paf=[FILE] derive precise alignments for this input
PAF
-W[N], --wflamda-segment=[N] wflambda segment length: size (in bp) of
segment mapped in hierarchical WFA
problem [default: 256]
-A[N], --wflamda-min=[N] minimum wavefront length (width) to
trigger reduction [default: 100]
-D[N], --wflambda-diff=[N] maximum distance that a wavefront may be
behind the best wavefront [default:
100000]
-C[N], --max-patch-major=[N] maximum length to patch in the major
axis [default: 512*segment-length]
-F[N], --max-patch-minor=[N] maximum length to patch in the minor
axis [default: 128*segment-length]
-E[N], --erode-math-mismatch=[N] maximum length of match/mismatch islands
to erode before patching [default: 13]
-d, --md-tag output the MD tag
-a, --sam-format output in the SAM format (PAF by
default)
-B[PATH], --tmp-base=[PATH] base name for temporary files [default:
`pwd`]
-T, --keep-temp keep intermediate files generated during
mapping and alignment
"--" can be used to terminate flag options and force all following
arguments to be treated as positional options
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