smalt command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

smalt: command not found

or when using sudo you get the following error message

sudo: smalt: command not found

Solutions to smalt: command not found

How To Fix smalt: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu smalt is provided by smalt package.

smalt is:

SMALT efficiently aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.

The software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant steps along the genomic reference sequences.

For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm.

The best gapped alignments of each read is reported including a score for the reliability of the best mapping. The user can adjust the trade-off between sensitivity and speed by tuning the length and spacing of the hashed words.

A mode for the detection of split (chimeric) reads is provided. Multi-threaded program execution is supported.

To fix this problem, we can install more using the command below.

sudo apt-get -y install smalt

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install smalt.

sudo apt -y install smalt

Or if you have aptitude installed you can use the following command.

sudo aptitude install smalt

Summary

In this tutorial we learn how to fix smalt command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.