---
name: "wham-build"
section: "1"
platform: "linux"
package: "wham-align"
version: "0.1.5-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/wham-build"
---

# wham-build(1)

Wisconsin's High-Throughput Alignment Method

## NAME

wham-build - Wisconsin's High-Throughput Alignment Method

## DESCRIPTION

### Usage:

-

  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

- **-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

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.