wtdbg-cns command not found

Introduction

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

wtdbg-cns: command not found

or when using sudo you get the following error message

sudo: wtdbg-cns: command not found

Solutions to wtdbg-cns: command not found

How To Fix wtdbg-cns: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu wtdbg-cns is provided by wtdbg2 package.

wtdbg2 is:

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.

During assembly, wtdbg2 chops reads into 1024bp segments, merges similar segments into a vertex and connects vertices based on the segment adjacency on reads. The resulting graph is called fuzzy Bruijn graph (FBG). It is akin to De Bruijn graph but permits mismatches/gaps and keeps read paths when collapsing k-mers. The use of FBG distinguishes wtdbg2 from the majority of long-read assemblers.

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

sudo apt-get -y install wtdbg2

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

You can also use apt command to install wtdbg2.

sudo apt -y install wtdbg2

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

sudo aptitude install wtdbg2

Summary

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