Bioinformatics Center

**This is an old revision of the document!**

In the terminal, you can see the list of available software packages by command 'modul avail'. A short list of available applications (13.01.2020) below:

 
 bamtools/2.5.1                      cufflinks/2.2.1         mothur/1.40.5              r/3.5.3
 bamutil/1.0.13                      datamash/1.3            openjdk/11.0.2             r/3.6.0
 bcftools/1.9                        diamond/0.9.21          openmpi/1.10.7-2           r/3.6.1           (D)
 bedtools2/2.27.1                    fastqc/0.11.7           picard/2.18.3              samtools/1.9
 blast-plus/2.7.1                    fastx-toolkit/0.0.14    plink/1.07                 sra-toolkit/2.9.2
 bowtie/1.2                          gcc/8.2.0               plink/1.90b6.12     (D)    star/2.5.1b
 bowtie/1.2.3                 (D)    hisat2/2.1.0            prinseq-lite/0.20.4        star/2.5.4b
 bowtie2/2.3.4.1-python-3.7.0        hmmer/3.0               python/2.7.15              star/2.6.1b       (D)
 breakdancer/master                  htslib/1.9              python/2.7.17              tabix/2013-12-16
 breakdancer/1.4.5            (D)    jdk/12.0.1              python/3.7.0               trimmomatic/0.36
 bwa/0.7.17                          matlab/R2018b           python/3.7.3        (D)    vcftools/0.1.14
 clustalw/2.1                        mono/5.4.1.7            r/3.5.1                    seqan/2.4.0
 kallisto/0.43.1                     homer/4.9.1             homer/4.10 (D)

Lmod Module Environment

Quick tutorial:

module avail

module load bowtie2

module load python/3.7.3

module unload bowtie2

module save

module restore

Application location

module load bowtie2
cd $BOWTIE2_ROOT