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| Version 47 (modified by , 5 years ago) (diff) |
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Available Software
Before any software can be used, the corresponding module has to be loaded. This is done by typing module load software_name. You can use module avail or module whatis to list the names of the available software modules. To list the modules currently loaded, use module list
In many cases you will need to submit your jobs to GridEngine. This is the case when the runtime exceeds 30 minutes or the memory requirement exceeds 2GB.
Please edit the software pages and add notes if you find the information incomplete, or if you want to share any specifics on how the software is used.
Alignment
- Software/Mafft - Multiple sequence alignment program (Version 7.450)
Classification
- Software/GraftM - Pipeline to identify and classify marker gene reads from metagenomic datasets (Version 0.12.2)
Graphs
- Software/Krona - Set of scripts to create Krona charts (Version May 2019)
Phylogeny
- Software/IQ-TREE - Efficient software for phylogenomic inference (Version 1.6.12)
- Software/Pplacer - Phylogenetic placement (Version 1.1.19)
Sequence analysis
- Software/Fxtract - Extract sequences from a fastx file given a subsequence or identifier (Version 2.3)
- Software/HMMER - Biosequence analysis using profile hidden Markov models (Version 3.2.1)
- Software/OrfM - A simple and not slow open reading frame (ORF) caller (Version 0.7.1)
Statistics
- Software/R - The R language for statistical computing (Versions: 3.6.0)
Python
Sequencing
Legacy
The following software and modules used to be available before the grid upgrade. They have not been tested on the new grid, but may work without any issues. If you need to use them. Please try out. To load them, first load the module load the module "legacy", and then the appropriate module. If the software fails, please ask create an issue here in Trac and ask for the software or drop a mail to Les.
AEGeAn/0.9.3 emboss/6.6.0 openmpi/2.0.3 (D) AEGeAn/0.9.4 (D) exabayes/1.5 openpyxl/2.2.2 PBSuite/14.6.24 exonerate/2.2.0 orthofinder/1.1.8 R/2.12.0 fastme/2.1.5 orthomcl/2.0.8 R/2.15.1 fastqc/0.10.1 p/mykopat-gbrowse R/3.0.2 (D) fastqc/0.11.5 (D) paml/4.7 R/3.2.0 faststructure/1.0 parallelfork/1.1 R/3.4.1 fastx_toolkit/0.0.13.2 pbh5tools/0.8.0 abyss/1.3.4 filespeclink/filespeclink pear/0.9.10 abyss/1.3.5_kmer128 flexbar/3.0.3 perl/5.16.1 abyss/1.3.5 frc_align/20130408 perl/5.16.2 (D) abyss/1.3.6_kmer128 freebayes/0.9.6 phylip/3.695 abyss/1.3.6 (D) freebayes/0.9.21 picardtools/1.107 amos/3.1.0 freebayes/1.0.0-19-gefe685d (D) picardtools/2.10.0 (D) antismash/2.0.2 gatk/2.8-1 pysam/0.7.4 antismash/3.0.5.1 (D) gatk/3.7.0 python/2.7.3 augustus/2.6.1 gatk/4.0.5.1 (D) python3/3.3.2 augustus/2.7 gcc/7.1.0 python3/3.3.3 augustus/3.0.3 (D) geneid/1.4.4_110113 pyvcf-py3/0.6.7 bamm/2.5.0 genometools/1.5.2 pyvcf/0.6.3 bamtools/2.2.3 glimmer/3.0.2 qiime/1.7.0 bcftools/1.2 glimmerhmm/3.0.2 qiime/1.8.0 beast/1.8.4 gmake/3.82 qiime/1.9.1 (D) bedtools/2.16.2 gmes/2.3e quast/2.3 bioperl/00-2.1.8 grinder/0.5.4 repseek/091209 bioperl/1.6.901-p5162 (D) gsnap/2013-11-27 rocker/1.1.12 biopython-py3/1.63 hdf5/1.8.13 salmon/0.9.1 biopython-py3/1.65 hisat2/2.0.4 samtools/0.1.18 biopython/1.60 hisat2/2.1.0 (D) samtools/1.2 biopython/1.64 hmmer2/2.3.2 samtools/1.8 (D) biopython/1.66 (D) hmmer3/3.0 scipy-py3/0.13.1 blasr/2014.07.09 htslib/1.8 scipy/0.11.0rc2 blast2go iprscan/4.8_db39 seqtk/seqtk blat/35 iqtree/1.5.5 sga/0.10.1 bowtie/0.12.9 jre/1.6.0_39 sina/1.2.11 bowtie2/2.0.0-beta7 jre/1.7.0_11 snap/2012-05-17 bowtie2/2.0.2 jre/1.7.0_51 soapdenovo/1.05 bowtie2/2.1.0 jre/1.8.0_60 (D) solexaqa/3.1.7 bowtie2/2.2.3 kallisto/0.45 spades/3.6.0 bowtie2/2.2.4 legacy-blast/2.2.26 structure/2.3.4 bowtie2/2.3.2 (D) libfuse3/3.2.0 structure/2.3.4.1 (D) bwa/0.5.10 mafft/6.94 tassel/5.0 bwa/0.6.2 matplotlib-py3/1.3.1 tophat/2.0.3.1 bwa/0.7.4 (D) matplotlib/1.2.0rc1 (D) tophat/2.0.6 bzip2c/1.0.6 mavid/2.0.4 tophat/2.0.9 cafe/2.2 mcl/12.068 tophat/2.0.11 cafe/3.1 (D) meme/4.10.0 tophat/2.0.13 (D) cdhit/4.6.1 mercator/2013.01.11 trac/1.0.1
