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| Version 97 (modified by , 2 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/Bowtie2 - Fast short read aligner
- Software/NCBI-BLAST+ - Local sequence alignment search tool
- Software/Diamond - Sequence aligner for protein and translated DNA searches
- Software/Exonerate - Sequence alignment tool, excels e.g. at spliced EST alignments
- Software/Infernal - Inference of RNA alignments
- Software/GmapGsnap - GMAP/GSNAP short read mapper/aligner for RNASeq and genomic data
- Software/Mafft - Multiple sequence alignment program
- Software/Mauve - Multiple alignment of genomes
- Software/Minimap2 - Long-read and genome to genome alignment tool
- Software/Salmon - RNASeq alignment and quantification tool
- Software/star - splicing-aware RNA alignment
Classification
- Software/GraftM - Pipeline to identify and classify marker gene reads from metagenomic datasets
Graphs
- Software/Krona - Set of scripts to create Krona charts (Version May 2019)
Phylogeny
- Software/CAFE - Evaluate gene family evolution within a species tree
- Software/epa-ng - Phylogenetic placement
- Software/exabayes - Massively parallel Bayesian phylogenetic analysis
- Software/FastTreeMP - Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
- Software/gappa - Placements of short environmental sequences on a reference phylogenetic tree
- Software/IQ-TREE - Phylogenetic tree inference tool
- Software/OrthoFinder - Infers orthogroups, gene trees of orthogroups and species trees from proteomes.
- Software/Pplacer - Phylogenetic placement
- Software/raxml-ng - Phylogenetic tree inference tool
- Software/SEPP - SATe-enabled Phylogenetic Placement
Sequence analysis
- Software/BUSCO - Software package to evaluate genome completeness.
- Software/Fxtract - Extract sequences from a fastx file given a subsequence or identifier
- Software/HMMER - Biosequence analysis using profile hidden Markov models
- Software/OrfM - A simple and not slow open reading frame (ORF) caller
- Software/RECON - Software for repeat finding in genomic sequences (please check Software/RepeatModeler)
- Software/RepeatScout - Software for repeat find in genomic sequences (please check Software/RepeatModeler)
- Software/RepeatMasker - The de facto standard software for repeat masking of genomic sequences
- Software/RepeatModeler - The de-novo repeat family identification and modeling package.
- Software/TRF - Software for finding tandem repeats in genomic sequences
- Software/mfqe - FASTA/FASTQ extractor for multiple sets of read names
- Software/BCFtools - Analysis and handling of VCF/BCF (Variant Call Format) files
- Software/BEDtools - Swiss Army knife for genomic analysis
- Software/Jellyfish - A fast k-mer counter
Sequence and Genome Annotation tools
- Software/Augustus - Gene pretiction
- Software/GeneMarkES -- Gene prediction
- Software/InterProScan - Functional annotation of gene sequences (5.48 with database release 83.0)
- Software/MAKER - MAKER genome annotation suite
- Software/MetaEuk - Sensitive, high-throughput gene discovery and annotation
- Software/Prodigal - Fast, reliable protein-coding gene prediction for prokaryotic genomes.
- Software/SNAP - Semi-HMM-based Nucleic Acid Parser. A gene prediction tool.
- Software/tRNAScan-SE - Annotate tRNAs in DNA sequence
Assembly tools -- genome and transcriptome assembly
- Software/ABySS - ABySS short read assembler
- Software/MEGAHIT - Megahit metagenome assembler
- Software/MetaBat2 - Metabat 2 metagenome assembly binning algorithm
- Software/SOAPdenovo2 - SOAPdenovo short read assembler
- Software/SPAdes - SPAdes short read de novo assembler
- Software/Trinity - Trinity RNASeq assembler
- Software/Velvet - Velvet short read assembler
Statistics
- Software/R - The R language for statistical computing
Perl
- Software/Perl - The Perl programming language
Python
Sequencing
Compilers, Libraries, and Other Misc software
- Software/NodeJS - Javascript runtime environment
- Software/OpenMPI
- Software/lbzip2
- Software/libxml2
- Software/parallel
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
