wham-build1
Wisconsin's high-throughput alignment method
Overview
Usage:
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wham-build [options]*
-l<int> <ref_sequence> <basepath>-l<int> specify the length of short reads <ref_sequence> comma-separated list of fiels with ref sequences <basepath> write wham data to files with this dir/basename
Options
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-v <int> -
report hits with <=v errors (0-5), ignore qualities
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-p <int> -
specify the number of fragments for alignments
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-m <int> -
discard subsequences appearing more than <int> times (default: 100).
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-b <int> -
specify the number of buckets
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-a -
find all valid matches (need much more memory)
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--mask -
keep masked characters in the sequences (default: on)
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--unmask -
discard masked characters in the sequences. Masks are treated as Ns
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--version -
print version information
-h/--help-
print this usage message
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).