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Bio Software

From CRC Wiki

General Description

 Loading the bio module will load the following modules
 Bismark
 Bowtie
 BWA - recommended for aln/sampe/samse
 Cutadapt
 FastQC
 Gatk
 HTSeq
 Picardtools
 Samtools
 Tophat
 Trimmomatic
 Two other modules can be loaded and/or swapped independently
 BWA version 0.7.12 - recommended for mem  
 Cutadapt version 1.8.3 - contains an option for paired reads
 For information on each module,including loading, please see that module's page.

Basic Usage

module avail bio

To load all bio modules:

module load bio

But to load just one bio module, i.e., tophat:

module load bio/tophat

Useful Options


Further Information

See the official website: [http:// ]