---
name: "kissreads2"
section: "1"
platform: "linux"
package: "discosnp"
version: "1:2.6.2-4+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kissreads2"
---

# kissreads2(1)

enhances the kissnp2 results by computing per read set

## NAME

kissreads2 - enhances the kissnp2 results by computing per read set

## DESCRIPTION

\[Kissreads2 options\]

- **-x**

  (0 arg) :    radseq option, homogeneous read depth along the prediction

- **-predictions**

  (1 arg) :    Input predictions

- **-reads**

  (1 arg) :    Input reads

- **-unco**

  (1 arg) :    Output uncoherent file name  \[default '/dev/null'\]

- **-co**

  (1 arg) :    Output coherent file name

- **-hamming**

  (1 arg) :    Maximal hamming distance authorized while maping  \[default '1'\]

- **-coverage\_file** (1 arg) :

  File (.h5) generated by kissnp2, containing the coverage threshold per read set  \[default '\_removemeplease'\]

- **-k**

  (1 arg) :    Size of k, used as minial overlap and kmer spanning read coherence  \[default '31'\]

- **-index\_stride**

  (1 arg) :    Index Stride  \[default '2'\]

- **-size\_seeds**

  (1 arg) :    Size of the used seeds (distinct from the size of k)  \[default '25'\]

- **-output\_fasta**

  (0 arg) :    Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline

- **-genotype**

  (0 arg) :    Compute genotypes

- **-nb-cores**

  (1 arg) :    number of cores  \[default '0'\]

- **-verbose**

  (1 arg) :    verbosity level  \[default '1'\]

- **-version**

  (0 arg) :    version

- **-help**

  (0 arg) :    help

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.