Difference between revisions of "Illumina-utils"

Latest revision as of 18:43, 15 August 2022

Description

This is a small library and a bunch of clients to perform various operations on FASTQ files (such as demultiplexing raw Illumina files, merging partial or complete overlaps, and/or performing quality filtering). It works with paired-end FASTQ files and has been tested with Illumina runs processed with CASAVA version 1.8.0 or higher.

Environment Modules

Run module spider illumina-utils to find out what environment modules are available for this application.

System Variables

HPC_ILLUMINA-UTILS_DIR - installation directory
HPC_ILLUMINA-UTILS_BIN - executable directory

Citation

If you publish research that uses illumina-utils you have to cite it as follows:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066643

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:biology]]
+[[Category:Software]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|illumina-utils}}
@@ 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
-* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 <!--Configuration-->
@@ Line 72: / Line 60: @@
 If you publish research that uses {{#var:app}} you have to cite it as follows:
-[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066643]
+http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066643
 |}}