Bio Softwares using EESSI
A large number of bioinformatics programs are readily available for Komondor users through the EESSI module.
The following software packages are accessible via environment modules:
Software |
Description |
Link |
|---|---|---|
BCFtools/1.17-GCC-12.2.0, BCFtools/1.18-GCC-12.3.0 (D) |
Manipulate and analyze genetic variant data in VCF/BCF formats. |
|
BLAST+/2.14.0-gompi-2022b, BLAST+/2.14.1-gompi-2023a (D) |
Compare biological sequences against databases to find homologs. |
|
BWA |
Align short high-throughput sequencing reads to a reference genome. |
|
BamTools/2.5.2 |
Tools and C++ API for working with BAM files. |
|
Bio-DB-HTS/3.01 |
Perl module for accessing HTS data. |
|
Bio-SearchIO-hmmer/1.7.3 |
BioPerl parser for HMMER output. |
|
BioPerl/1.7.8 (D) |
Perl modules for biological computation. |
|
Biopython/1.81, 1.83 (D) |
Python tools for biological computation. |
|
Bowtie2/2.5.1 |
Ultrafast tool for aligning sequencing reads. |
|
CD-HIT/4.8.1 |
Cluster protein or nucleotide sequences. |
|
Cassiopeia/2.0.0 |
Reconstruct single-cell lineages. |
|
DIAMOND/2.1.8 |
Fast protein aligner, BLAST-compatible. |
|
DendroPy |
Python library for phylogenetic analysis. |
|
ETE/3.1.3 |
Toolkit for phylogenetic trees. |
|
FragGeneScan/1.31 |
Predict genes in fragmented metagenomic reads. |
|
Tombo/1.5.1 |
Detect DNA modifications in nanopore data. |
|
Transrate/1.0.3 |
Evaluate de novo transcriptome assemblies. |
|
VCFtools/0.1.16 |
Tools for VCF file analysis. |
|
VSEARCH/2.30.0 |
Versatile tool for metagenomics. |
|
WhatsHap (D) |
Phase variants using long reads. |
|
bcgTree/1.2.1 |
Build bacterial core genome trees. |
|
crb-blast/0.6.9 |
Check redundancy in BLAST hits. |
|
cutadapt/5.0 |
Trim adapters and low-quality bases. |
|
GATK/4.5.0.0 |
Variant calling toolkit from Broad Institute. |
|
fastp/0.23.4 |
Fast preprocessing for FASTQ files. |
|
GROMACS/2024.x |
Molecular dynamics simulation suite. |
|
Gblocks/0.91b |
Eliminate unreliable alignment regions. |
|
GenomeTools/1.6.2 |
Genome analysis toolkit. |
|
HMMER/3.4 |
Profile HMM-based sequence searches. |
|
HTSlib |
Library for reading/writing sequencing data. |
|
hic-straw/1.3.1 |
Parse Hi-C interaction data. |
|
IQ-TREE/2.3.5 |
Phylogenetic tree inference using ML. |
|
KronaTools/2.8.1 |
Interactive metagenomic visualization. |
|
MAFFT |
Multiple sequence alignment program. |
|
MDAnalysis/2.4.2 |
Analyze molecular dynamics trajectories. |
|
MEGAHIT/1.2.9 |
Ultra-fast metagenomic assembler. |
|
MMseqs2/14-7e284 |
Fast sequence search and clustering. |
|
MUSCLE/5.1.0 |
Multiple sequence alignment. |
|
Mash/2.3 |
Genome distance estimation using MinHash. |
|
MetaEuk/6 |
Gene prediction in metagenomics. |
|
MultiQC/1.14 |
Summarize QC reports across samples. |
|
Nextflow |
Workflow language for reproducible pipelines. |
|
OrthoFinder/2.5.5 |
Determine orthogroups and species trees. |
|
ncbi-vdb |
Tools to access NCBI SRA data. |
|
Pysam |
Python bindings for SAMtools and HTSlib. |
|
pyfaidx |
Random access to FASTA files. |
|
R-bundle-Bioconductor |
Genomic analysis packages for R. |
|
RAxML |
Phylogenetic inference using ML. |
|
SAMtools |
Tools for manipulating alignments. |
|
SEPP |
Place short sequences into reference trees. |
Last update by Milán SZŐRI: 2025-06-15