wham-build - Wisconsin's High-Throughput Alignment Method
- 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
- -v <int>
- report hits with <=v errors (0-5), ignore qualities
- -p <int>
- specify the number of fragments for alignments
- -m <int>
- discard subsequences appearing more than <int> times (default:
100).
- -b <int>
- specify the number of buckets
- -a
- find all valid matches (need much more memory)
- --mask
- keep masked characters in the sequences (default: on)
- --unmask
- discard masked characters in the sequences. Masks are treated as Ns
- --version
- print version information
- -h/--help
- print this usage message
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.