Difference between revisions of "Fqtools"

Latest revision as of 16:47, 15 August 2022

Description

fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual subcommands will take either a single file or a pair of files as input. If no input file is specified, fqtools will attempt to read data from stdin. In this case, it is advisabe to specify the format of the data provided. For subcommands that generate FASTQ data, either a single file or a pair of files will be generated. If no -o argument is provided, single files will be writted to stdout.

Environment Modules

Run module spider fqtools to find out what environment modules are available for this application.

System Variables

HPC_FQTOOLS_DIR - installation directory

Citation

If you publish research that uses fqtools you have to cite it as follows:

Droop, A. P. (2016). fqtools: An efficient software suite for modern FASTQ file manipulation. Bioinformatics (Oxford, England).

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|fqtools}}
@@ Line 21: / Line 21: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* gcc/5.2.0
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==