samclip command not found

In this troubleshooting guide we learn how to fix samclip command not found error message

Introduction

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

samclip: command not found

or when using sudo you get the following error message

sudo: samclip: command not found

Solutions to samclip: command not found

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

In Ubuntu samclip is provided by samclip package.

samclip is:

Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in –end-to-end mode). This means the ends of the read may not be part of the best alignment.

This can be caused by:

  • adapter sequences (aren’t in the reference)
  • poor quality bases (mismatches only make the alignment score worse)
  • structural variation in your sample compared to the reference
  • reads overlapping the start and end of contigs (including circular genomes)

Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which describes which parts of the read aligned and which didn’t. The unaligned ends of the read can be “soft” or “hard” clipped, denoted with S and H at each end of the CIGAR string. It is possible for both types to be present, but that is not common. Soft and hard don’t mean anything biologically, they just refer to whether the full read sequence is in the SAM file or not.

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

sudo apt-get -y install samclip

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

You can also use apt command to install samclip.

sudo apt -y install samclip

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

sudo aptitude install samclip

Summary

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