---
name: "cm_to_wigeon"
section: "1"
platform: "linux"
package: "wigeon"
version: "20101212+dfsg1-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cm_to_wigeon"
---

# cm\_to\_wigeon(1)

helper for wigeon (Pintail 16S DNA anomaly detection)

## NAME

cm\_to\_wigeon - helper for wigeon (Pintail 16S DNA anomaly detection)

## DESCRIPTION

**Unfortunately this tools that comes in connection with [wigeon(1)](/wigeon/1.md)** **is not documented but it regards the options below.  If you know** **better about its purpose please drop us a note using reportbug on** **your Debian system.**

## OPTIONS

### Required:

- **--query\_NAST**

  multi-fasta file containing query sequences in alignment format

- **--db\_NAST**

  db in NAST format

- **--db\_FASTA**

  db in fasta format (megablast formatted)

### Common options

- **-n**

  number of top matching database sequences to compare to (default 15)

- **-R**

  min divergence ratio default: 1.007

- **-P**

  min percent identity among matching sequences (default 90)

### Parameters to tune ChimeraMaligner:

Scoring parameters:

- **-M**

  match score   (default: +5)

- **-N**

  mismatch penalty  (default: **-4**)

- **-Q**

  min query coverage by matching database sequence (default: 70)

- **-T**

  maximum traverses of the multiple alignment  (default: 1)

### Flags:

- **--printAlignments**

  (default off)

- **-v**

  verbose

- **--exec\_dir**

  cd here before running

## SEE ALSO

http://microbiomeutil.sourceforge.net/

## AUTHOR

This manual page was written by Andreas Tille \<tille@debian.org\> but can be freely used for any other distribution.