sqt command not found

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

Introduction

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

sqt: command not found

or when using sudo you get the following error message

sudo: sqt: command not found

Solutions to sqt: command not found

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

In Ubuntu sqt is provided by python3-sqt package.

python3-sqt is:

sqt is a collection of command-line tools for working with high-throughput sequencing data. Conceptionally not fixed to use any particular language, many sqt subcommands are currently implemented in Python. For them, a Python package is available with functions for reading and writing FASTA/FASTQ files, computing alignments, quality trimming, etc.

The following tools are offered:

  • sqt-coverage – Compute per-reference statistics such as coverage and GC content
  • sqt-fastqmod – FASTQ modifications: shorten, subset, reverse complement, quality trimming.
  • sqt-fastastats – Compute N50, min/max length, GC content etc. of a FASTA file
  • sqt-qualityguess – Guess quality encoding of one or more FASTA files.
  • sqt-globalalign – Compute a global or semiglobal alignment of two strings.
  • sqt-chars – Count length of the first word given on the command line.
  • sqt-sam-cscq – Add the CS and CQ tags to a SAM file with colorspace reads.
  • sqt-fastamutate – Add substitutions and indels to sequences in a FASTA file.
  • sqt-fastaextract – Efficiently extract one or more regions from an indexed FASTA file.
  • sqt-translate – Replace characters in FASTA files (like the ’tr' command).
  • sqt-sam-fixn – Replace all non-ACGT characters within reads in a SAM file.
  • sqt-sam-insertsize – Mean and standard deviation of paired-end insert sizes.
  • sqt-sam-set-op – Set operations (union, intersection, …) on SAM/BAM files.
  • sqt-bam-eof – Check for the End-Of-File marker in compressed BAM files.
  • sqt-checkfastqpe – Check whether two FASTQ files contain correctly paired paired-end data.

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

sudo apt-get -y install python3-sqt

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

You can also use apt command to install python3-sqt.

sudo apt -y install python3-sqt

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

sudo aptitude install python3-sqt

Summary

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