---
name: "reapr-smaltmap"
section: "1"
platform: "linux"
package: "reapr"
version: "1.0.18+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/reapr-smaltmap"
---

# reapr-smaltmap(1)

map read pairs using SMALT

## NAME

reapr-smaltmap - map read pairs using SMALT

## SYNOPSIS

**reapr smaltmap** \[options\] \<assembly.fa\> \<reads\_1.fastq\> \<reads\_2.fastq\> \<out.bam\>

## DESCRIPTION

Maps read pairs to an assembly with SMALT, making a final BAM file that is sorted, indexed and has duplicates removed.

The n-th read in \<reads\_1.fastq\> should be the mate of the n-th read in \<reads\_2.fastq\>.

It is assumed that reads are 'innies', i.e. the correct orientation is reads in a pair pointing towards each other (--→ ←--).

## OPTIONS

- **-k** \<int\>

  The -k option (kmer hash length) when indexing the genome with 'smalt index' \[13\]

- **-s** \<int\>

  The -s option (step length) when indexing the genome with 'smalt index' \[2\]

- **-m** \<int\>

  The -m option when mapping reads with 'smalt map' \[not used by default\]

- **-n** \<int\>

  The number of threads used when running 'smalt map' \[1\]

- **-y** \<float\>

    The -y option when mapping reads with 'smalt map'. The default of 0.5 means that at least 50% of each read must map perfectly. Depending on the quality of your reads, you may want to increase this to be more stringent (or consider using -m) \[0.5\]

- **-x**

    Use this to just print the commands that will be run, instead of actually running them

- **-u** \<int\>

      The -u option of 'smalt sample'. This is used to estimate the insert size from a sample of the reads, by mapping every n^th read pair \[1000\]

## SEE ALSO

[reapr(1)](/reapr/1.md)