seqsero_batch_pair-end command not found

In this troubleshooting guide we learn how to fix seqsero_batch_pair-end command not found error message

Introduction

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

seqsero_batch_pair-end: command not found

or when using sudo you get the following error message

sudo: seqsero_batch_pair-end: command not found

Solutions to seqsero_batch_pair-end: command not found

How To Fix seqsero_batch_pair-end: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu seqsero_batch_pair-end is provided by seqsero package.

seqsero is:

SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.

SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing

  1. raw reads from genomes of 308 Salmonella isolates of known serotype
  2. raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and
  3. 354 other publicly available draft or complete Salmonella genomes. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.

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

sudo apt-get -y install seqsero

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

You can also use apt command to install seqsero.

sudo apt -y install seqsero

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

sudo aptitude install seqsero

Summary

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