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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Bio-apps

Bio-apps provides access to a large collection of bioinformatics applications on Roihu, installed as environment modules. It is the successor to the biokit collection on the decommissioned Puhti and Mahti systems.

Bio-apps is opt-in: loading the bio-apps module adds the bioinformatics application module tree to your MODULEPATH, after which you can find and load individual applications with the normal module commands. Loading bio-apps does not load any application itself — it only makes them available for loading.

Bio-apps environment is not yet fully tested

Some software in the bio-apps environment is not yet fully tested, and might not have a corresponding page in Docs CSC yet. Use these apps with caution, and reach out to CSC Service Desk for any issues that you face.

Available

Bio-apps is available on Roihu:

  • bio-apps/v202603

The same bio-apps/v202603 command works on both CPU and GPU (GH200) nodes. The node you are on selects the matching software: a broad set of applications on CPU nodes, and a small set of GPU-accelerated tools on GPU nodes.

Usage

Load the bioinformatics application module tree with:

module load bio-apps/v202603

Loading bio-apps makes the application modules available, but does not load the applications themselves.

List the available bioinformatics modules with:

module avail

Search for a particular application with module spider. For example:

module spider samtools

Load the required application after loading bio-apps:

module load samtools/1.21

You can then use the application normally:

samtools --version

To remove an application from your environment, unload its module:

module unload samtools

When you no longer need the bioinformatics module tree, unload bio-apps:

module unload bio-apps

See the specific application documentation for more information about finding, loading and using individual software modules in bio-apps.

Included applications

The collection contains applications for, among other things:

  • sequence quality control and preprocessing
  • sequence alignment and read mapping
  • genome and transcriptome assembly
  • SAM, BAM, BED and VCF processing
  • variant calling
  • genome annotation and gene prediction
  • metagenomics and taxonomic classification
  • phylogenetics and population genetics
  • multiple sequence alignment
  • workflow management
  • access to biological sequence archives

CPU nodes

The following modules are included in bio-apps/v202603 on Roihu CPU nodes:

abyss/2.3.10
admixtools/8.0.2
admixture/1.4.0
angsd/0.940
antismash/8.0.4
astral/5.7.1
augustus/3.5.0
bamtools/2.5.2
barrnap/0.9
bbmap/39.59
bcftools/1.23.1
beast2/2.6.7
bedops/2.4.42
bedtools2/2.31.1
blast-plus/2.17.0
boost/1.86.0
bowtie/1.3.1
bowtie2/2.5.4
bracken/2.9
braker4/0.5.0-beta
busco/5.4.3
busco/6.1.0
bwa/0.7.19
bwa-mem2/2.3
canu/2.2
cdhit/4.8.1
checkm2/1.1.0
clumpp/1.1.2
clustal-omega/1.2.4
clustalw/2.1
cufflinks/2.2.1
diamond/2.1.10
eggnog-mapper/2.1.15
emboss/6.6.0
exonerate/2.4.0
fastp/1.0.1
fastqc/0.12.1
fastx-toolkit/0.0.14
freebayes/1.3.6
gapseq/2.1.0
gatk/4.5.0.0
getorganelle/1.7.7.1
hisat2/2.2.1
hmmer/3.4
htslib/1.23.1
humann/4.0.0a2
hybpiper/2.3.4
hyphy/2.5.51hf
igv/2.19.7
iq-tree/2.4.0
jellyfish/2.2.7
kraken2/2.17.1
mafft/7.525
mash/2.3
megahit/1.2.9
meme/5.5.7
metabat/2.15
minimap2/2.30
mmseqs2/18-8cc5c
mothur/1.48.0
mrbayes/3.2.7a
mummer4/4.0.1
muscle/3.8.31
muscle5/5.1.0
ncbi-toolkit/28_0_12
nextflow/25.10.2-standalone
openmpi/5.0.10-gcc14.3.0
perl-bioperl/1.7.8
phylip/3.697
picard/3.3.0
plink/1.07
plink2/2.0.0-a.6.9
prodigal/2.6.3
py-biopython/1.85
py-cutadapt/4.7
py-dbcan/5.2.9
py-deeptools/3.5.3
py-gtdbtk/2.7.2
py-htseq/2.0.3
py-instrain/1.6.3
py-ipyrad/0.9.102
py-metaphlan/4.2.4
py-micom/0.39.0
py-multiqc/1.28
py-steadiercom/0.1.5
raxml/8.2.12
raxml-ng/2.0.2
roary/3.13.0
samtools/1.21
seqkit/2.10.0
seqtk/1.4
snakemake/7.32.4
snakemake/9.14.0
sortmerna/7.0.0
spades/4.2.0
sra-tools/3.3.0
star/2.7.11b
strauto/1.0
stringtie/3.0.3
structure/2.3.4
structureharvester/0.7
tophat/2.1.2
trimmomatic/0.39
trinity/2.15.1.FULL
vcftools/0.1.17
vsearch/2.22.1

GPU nodes (GH200)

On Roihu GPU nodes, bio-apps/v202603 provides a small set of GPU-accelerated tools:

dorado/2.1.1
mmseqs2/18-8cc5c
nextflow/25.10.2-standalone
py-medaka/2.2.2
snakemake/7.32.4
snakemake/9.14.0

License

The applications included in Bio-apps are distributed under their own licenses. Most are free and open-source software, but license and citation requirements differ between applications.

Consult the documentation and license information of each application before using or redistributing it.

Citation

See above. See each application page for citation guidelines.

Support

Application-specific usage instructions will be made available on the corresponding page in the CSC application catalog.

For problems related to the Bio-apps module tree or an included application, contact CSC Service Desk.